@article {pmid42365126,
year = {2026},
author = {Choi, I and Kim, S and Baek, I},
title = {Advances and clinical potential of epigenome editing.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {42365126},
issn = {1420-9071},
support = {RS-2023-00278378//Ministry of Science and ICT, South Korea/ ; RS-2025-02217909//Ministry of Science and ICT, South Korea/ ; RS-2026-25478918//Ministry of Science and ICT, South Korea/ ; },
mesh = {Humans ; *Epigenome Editing/methods ; Animals ; CRISPR-Cas Systems/genetics ; *Epigenesis, Genetic ; *Epigenome ; Precision Medicine/methods ; Chromatin/genetics/metabolism ; Neoplasms/genetics/therapy ; },
abstract = {Epigenome editing has emerged as a powerful platform to modulate gene expression in a precise and reversible manner. Recent advances have significantly improved the efficiency, specificity, and durability of epigenome editing systems, enabling fine-tuned transcriptional control. Building on these developments, epigenome editing platforms are now being explored for therapeutic applications. In this review, we summarize the evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based epigenome editing technologies, highlighting key improvements in effector modules. We then discuss the disease models in which epigenome editing has been applied, including monogenic disorders, cancer, neurological diseases, and chronic diseases. These examples demonstrate the broad therapeutic promise of targeted epigenetic modulation across diverse pathological contexts. Finally, we tackle key barriers to clinical translation, including cell-type and chromatin context-specific design, in vivo delivery, and multi-gene targeting for complex disease. Collectively, this review underscores the potential of epigenome editing as a versatile platform for precision medicine.},
}

Humans
*Epigenome Editing/methods
Animals
CRISPR-Cas Systems/genetics
*Epigenesis, Genetic
*Epigenome
Precision Medicine/methods
Chromatin/genetics/metabolism
Neoplasms/genetics/therapy

@article {pmid42420452,
year = {2026},
author = {Al-Zahrani, KN and Langille, ER and Nurtanto, J and Obersterescu, A and Teng, K and Lowden, C and Dessapt, J and Chiu, CH and Caldwell, LV and Cook, DP and Pérez-Castro, MA and Berman, JM and Tsai, R and Bahcheli, AT and Mbamalu, G and Wu, S and Narimatsu, M and Lopes, AG and Fotiadou, I and Chan, K and Zhang, L and Bang, KWA and Parsons, MJ and Mourao, L and Temel, EI and McCulla, L and Sravya, P and Zhang, L and Sajjakulnukit, P and Lyssiotis, CA and Borowsky, AD and Scheele, CLGJ and Wahl, DR and Jackson, HW and Stewart, KS and Fuchs, E and Egan, SE and Pujana, MA and Reimand, J and Wrana, JL and Schramek, D},
title = {Aneuploidy selects for the acquisition of driver genes in breast cancer.},
journal = {Nature},
volume = {657},
number = {8132},
pages = {800-810},
pmid = {42420452},
issn = {1476-4687},
mesh = {Animals ; *Aneuploidy ; Female ; *Breast Neoplasms/genetics/pathology ; Humans ; Mice ; *Oncogenes/genetics ; CRISPR-Cas Systems/genetics ; DNA Copy Number Variations/genetics ; Signal Transduction/genetics ; Disease Models, Animal ; Reactive Oxygen Species/metabolism ; Tumor Suppressor Protein p53/genetics ; *Genes, Neoplasm/genetics ; Mitochondria/metabolism ; },
abstract = {Chromosome instability is highly prevalent in cancer and drives large-scale chromosomal imbalances, known as aneuploidies[1-4]. How aneuploidy contributes to tumorigenesis remains difficult to study due to the vast numbers of genes affected. Here we established a CRISPR knockout- and activation-linked assay (CRISPR-KOALA), enabling high-throughput bidirectional genetic screens in immunocompetent mouse models of cancer. We developed a compendium of the ten most frequent human chromosome-arm-level alterations in basal-like breast cancer (BLBC), a disease type that is driven by large copy-number alterations (CNAs)[5-8]. Using CRISPR-KOALA, we screened the mouse orthologues of 3,752 genes on these arms and identified 90 cancer driver genes, the function of the vast majority of which is unknown. These genes drive distinct signalling pathways including MAPK, HIPPO and WNT, reflecting the high degree of BLBC heterogeneity. Manipulating the identified cancer driver genes overcomes the need for CNAs in Trp53-mutant BLBC mouse models. Mechanistically, we identify that PLGRKT is a potent oncogene that lies on chromosome 9p and show that its tumour-promoting activity is associated with highly stress-resistant mitochondria and an increased ability to detoxify reactive oxygen species. Together, our findings reveal that arm-level CNAs can function to select specific driver genes to promote heterogeneous biological processes.},
}

Animals
*Aneuploidy
Female
*Breast Neoplasms/genetics/pathology
Humans
Mice
*Oncogenes/genetics
CRISPR-Cas Systems/genetics
DNA Copy Number Variations/genetics
Signal Transduction/genetics
Disease Models, Animal
Reactive Oxygen Species/metabolism
Tumor Suppressor Protein p53/genetics
*Genes, Neoplasm/genetics
Mitochondria/metabolism

@article {pmid42552655,
year = {2026},
author = {Wang, Y and Xu, H and Lu, W and Wan, Z and Xu, Z and Wang, W and Chen, C and Pan, E and Jiang, F and Liu, T and Li, Y and Xiao, D and Yang, X and Li, F and Hou, X and Zhang, C},
title = {Establishment of an efficient and PAM-relaxed LbCas12a genome editing tool in plants.},
journal = {The New phytologist},
volume = {252},
number = {2},
pages = {936-949},
pmid = {42552655},
issn = {1469-8137},
support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; CARS-23-A-16//National vegetable industry technology system/ ; HUNONGKE AI-A [2025] 004//Shanghai Academy of Agricultural Sciences AI-Empowered Agriculture Special Project/ ; 2025B02008//Key R&D Program of Xinjiang Uygur Autonomous Region/ ; CAAS-BRC-CB-2025-02//The Agricultural Science and Technology Innovation Program, the Basic Research Center/ ; JBGS[2021]064//Jiangsu Seed Industry Revitalization Project/ ; 2022YFD1200502//National Key Research and Development Program of China/ ; },
mesh = {*Genome, Plant/genetics ; Oryza/genetics ; Solanum lycopersicum/genetics ; Brassica/genetics ; Base Sequence ; *Nucleotide Motifs/genetics ; Mutation/genetics ; *CRISPR-Cas Systems/genetics ; Plants, Genetically Modified ; Genetic Engineering/methods ; *Gene Editing/methods ; *CRISPR-Associated Proteins/metabolism ; Bacterial Proteins ; Endodeoxyribonucleases ; },
abstract = {Cas12a is widely used in plant genome editing, but its targeting scope is constrained by stringent protospacer adjacent motif (PAM) requirements and variable activity across species, limiting its application at diverse genomic loci. LbCas12a-RRV-based editing system was established in nonheading Chinese cabbage, and T5exo-PF-LbCas12a was generated by introducing a triple mutation (D535G/S551F/D665N) and fusing with T5 exonuclease. This engineered system recognizes an expanded PAM sequence from 5'-VTTV-3' to 5'-NYHV-3'. The system exhibited efficient editing at noncanonical PAM sites in cabbage, tomato, and rice. Additionally, it successfully mediated large-fragment deletions via microhomology-mediated end joining (MMEJ) in plants. This study expands Cas12a targeting scope in plants and provides the first evidence for Cas12-mediated MMEJ-based large-fragment deletion. The toolkit facilitates functional genomics and crop improvement, and the methodology is readily adaptable to other plant species.},
}

*Genome, Plant/genetics
Oryza/genetics
Solanum lycopersicum/genetics
Brassica/genetics
Base Sequence
*Nucleotide Motifs/genetics
Mutation/genetics
*CRISPR-Cas Systems/genetics
Plants, Genetically Modified
Genetic Engineering/methods
*Gene Editing/methods
*CRISPR-Associated Proteins/metabolism
Bacterial Proteins
Endodeoxyribonucleases

@article {pmid42557315,
year = {2026},
author = {Neiswender, JV and Maffa, S and Brenan, L and ElHarouni, D and Yun, Y and Boyle, I and Wienand, K and Inam, H and Bertea, T and Anderson, A and Wong, M and Enriquez, M and Lenz, E and Villafranca, B and Shanks, N and Hager, M and Lloyd, N and Shadmany, H and Wie, SJ and Liang, H and Yunghans, K and Zhang, X and Golden, L and Harris, H and Day, S and Montgomery, P and Stokes, S and Giglio, RM and Hajal, C and Whittle, JR and Garcia, G and Mills, CE and Touat, M and Pelton, K and Li, H and Prabhakar, PS and Herter, S and Kamrat, ZH and Gui, D and Dilly, J and Wong, CK and Guo, JA and Pal, S and Baidi, Y and Johnston, R and Brown, DD and Bhatia, S and Winter, PS and Raghavan, S and Beroukhim, R and Colas, E and Spector, DL and Bass, AJ and Sorger, PK and Chen, Y and Hill, SJ and Oesterreich, S and Lee, AV and Beltran, H and Boehm, JS and Tseng, YY and Root, DE and Hahn, WC and Aguirre, AJ and Campbell, CD and Ligon, KL and Dempster, JM and Shibue, T and Vazquez, F},
title = {A dependency map enhanced with next-generation 3D cancer models.},
journal = {Nature},
volume = {657},
number = {8132},
pages = {789-799},
pmid = {42557315},
issn = {1476-4687},
mesh = {Humans ; *Neoplasms/genetics/pathology/classification/drug therapy ; Spheroids, Cellular/metabolism/pathology ; Animals ; Cell Line, Tumor ; *Models, Biological ; Multiomics ; Genomics ; CRISPR-Cas Systems/genetics ; Biomarkers, Tumor/genetics ; Gene Expression Regulation, Neoplastic ; },
abstract = {Despite advances in precision oncology, effective personalized treatments are still lacking for most patients with cancer[1]. The Cancer Dependency Map (DepMap) accelerates this field by systematically identifying cancer vulnerabilities in diverse preclinical models. Data from over 1,300 cell lines have led to the discovery of new therapeutic strategies across multiple tumour types[2]. However, mapping cancer vulnerabilities using traditional cell lines has limitations, including insufficient cancer subtype representation and the impact of culture conditions on perturbation responses. Here we perform 147 genome-scale CRISPR screens and multi-omic characterizations of next-generation (NextGen) cancer models (organoids and spheroids) across 10 cancer types. This strategy enables the expansion of DepMap to cover new genomic and molecular subtypes and to identify new biomarker-associated vulnerabilities. These new models also preserve transcriptional programs that are silenced in traditional cell lines and facilitate the discovery of specific gene dependencies associated with these programs. Comparisons of traditional and NextGen cancer models enable further identification of distinct effects of growth format and culture medium on gene essentiality. The integrated dataset combines data from both model types to offer a valuable, expansive resource for exploring cancer vulnerabilities and is accessible via the DepMap portal.},
}

Humans
*Neoplasms/genetics/pathology/classification/drug therapy
Spheroids, Cellular/metabolism/pathology
Animals
Cell Line, Tumor
*Models, Biological
Multiomics
Genomics
CRISPR-Cas Systems/genetics
Biomarkers, Tumor/genetics
Gene Expression Regulation, Neoplastic

@article {pmid42557320,
year = {2026},
author = {Herranz-Ors, C and Bhosle, SG and Beck, AE and Gilbert, JGR and Picco, G and Espejo Valle-Inclan, J and Muyas, F and Valentini, S and Andres, AE and Ansari, R and Barthorpe, S and Battarbee, G and Beaver, CM and Brocklesby, S and Cantwell, J and Collins, CA and Davis, J and Dimitrova, HG and Doran, J and Efendi, E and Evans, K and Fekry, M and Fowler, TA and Garcia-Casado, M and Griffiths, JAT and Hall, C and Hamer, R and Hardy, C and Hewitson, Z and Hitch, E and Holland, L and Jackson, DA and Joshi, N and Kavasakali, A and Letchford, L and Lightfoot, HB and Lingala, H and Mali, I and May, K and Mironenko, T and Morris, J and Pacini, C and Price, S and Robert-Tissot, G and Rogers, HA and Smith, JV and Smith, K and Souster, E and Spence, WJ and Thomas, F and Vieira, SF and Walker, S and Alfonsin, G and Bermingham, H and Coles, H and Ennis, DP and Freeman, A and Giannone, G and Grehan, N and Griffiths, EA and Hall, J and Lee, SL and Leung, EYL and Loreno, C and Millington, C and Mirnezami, A and Nutzinger, B and Orzechowska, K and Pinna, CMA and Redmond, AM and Roberts, K and Roy, S and Sanders, DA and Taniere, P and Vias, M and Wanigasooriya, K and , and Stratton, MR and Staudt, LM and McDermott, U and Brenton, JD and McNeish, IA and Biankin, A and Sansom, OJ and Cortes-Ciriano, I and Underwood, TJ and Fitzgerald, RC and Beggs, AD and Francies, HE and Garnett, MJ},
title = {A tumour-derived organoid biobank maps cancer gene dependencies.},
journal = {Nature},
volume = {657},
number = {8132},
pages = {765-774},
pmid = {42557320},
issn = {1476-4687},
mesh = {Humans ; *Organoids/metabolism/pathology ; *Neoplasms/genetics/pathology/drug therapy ; *Biological Specimen Banks ; Female ; *Genes, Neoplasm/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; Genes, Essential/genetics ; Precision Medicine ; ErbB Receptors/metabolism ; CRISPR-Cas Systems/genetics ; Alleles ; Colorectal Neoplasms/genetics/pathology ; ras Proteins/metabolism ; },
abstract = {Cancer cell lines remain foundational for research and drug discovery, yet they incompletely capture tumour diversity, lack linked patient context, and have undergone adaptation to culture. Tumour organoids are three-dimensional cultures derived from patient tissue that offer a powerful complement to cell lines[1]. Here we derived and characterized 256 clinically annotated tumour organoids directly from colorectal, oesophageal, ovarian, pancreatic and gastric cancers as renewable, genetically stable models. Extensive characterization of each model and matched patient tumour samples included whole-genome and transcriptome sequencing, and genome-wide CRISPR-Cas9 screens across 162 organoids mapped gene dependencies. Integrative analyses revealed genomic and clinical markers of dependency across common and rare subtypes, identified organoid-specific essential genes, and revealed targetable vulnerabilities following tumour evolution in paired pre- and post-treatment samples. In colorectal cancer, functional and pharmacological interrogation of the EGFR-RAS-MAPK axis uncovered differential effects of KRAS variant alleles. This open, publicly available resource provides a systematic map of gene dependencies in patient-derived organoids, expanding the model diversity and mechanistic insight needed to advance precision oncology.},
}

Humans
*Organoids/metabolism/pathology
*Neoplasms/genetics/pathology/drug therapy
*Biological Specimen Banks
Female
*Genes, Neoplasm/genetics
Proto-Oncogene Proteins p21(ras)/genetics
Genes, Essential/genetics
Precision Medicine
ErbB Receptors/metabolism
CRISPR-Cas Systems/genetics
Alleles
Colorectal Neoplasms/genetics/pathology
ras Proteins/metabolism

@article {pmid42557325,
year = {2026},
author = {Lee, JH and Li, Z and Soto, JS and Kim, AR and Illouz, T and Polonio, CM and Kilian, M and Kenison, JE and Schüle, AM and Akl, CF and Lee, HG and Andersen, BM and Ye, JJ and Rone, JM and Piester, G and Srun, L and Martinez, J and Danko, A and Lee, J and Heo, TH and Chung, EN and Oetjen, LK and Duart-Abadia, P and Koo, N and Perrimon, N and Wheeler, MA and Khakh, BS and Zandee, SEJ and Prat, A and Quintana, FJ},
title = {Antigen presentation by CD40[+]MHC-II[+] astrocytes promotes CNS autoimmunity.},
journal = {Nature},
volume = {657},
number = {8132},
pages = {755-764},
pmid = {42557325},
issn = {1476-4687},
mesh = {Animals ; *Astrocytes/immunology/metabolism/cytology ; *CD40 Antigens/immunology/metabolism ; Encephalomyelitis, Autoimmune, Experimental/immunology/pathology ; *Autoimmunity/immunology ; Mice ; Female ; *Antigen Presentation/immunology ; CD40 Ligand/metabolism/immunology ; *Central Nervous System/immunology/cytology ; CD4-Positive T-Lymphocytes/immunology ; *Histocompatibility Antigens Class II/immunology/metabolism ; Th17 Cells/immunology ; Humans ; Male ; Multiple Sclerosis/immunology/pathology ; Coculture Techniques ; Mice, Inbred C57BL ; CRISPR-Cas Systems ; },
abstract = {Astrocytes contribute to the pathology of multiple neurological disorders, including the T cell-driven autoimmune disease of the central nervous system (CNS) multiple sclerosis and its mouse model, experimental autoimmune encephalomyelitis[1]. However, little is known about functional interactions between astrocytes and CD4[+] T cells. Here using rabies barcode interaction detection followed by sequencing[2], in combination with single-cell RNA sequencing, in vitro co-culture systems and cell-specific in vivo CRISPR-Cas9-based genetic perturbation studies, we established that astrocytes expressing CD40 and MHC-II promote CNS T cell autoimmunity. We harnessed universal labelling immune partnerships by SorTagging intercellular contacts[3] to analyse astrocyte-interacting CD4[+] T cells, finding that direct astrocyte-CD4[+] T cell interactions enhance pathogenic T helper 17 cell responses in experimental autoimmune encephalomyelitis. In addition, we studied the effect of these interactions on astrocytes. Using in vivo subproteomic approaches[4] and AlphaFold-Multimer predictions[5], we established that CD40 activation in astrocytes by CD40L expressed by CD4[+] T cells induces the accumulation of PLIN4-positive lipid droplets, which provide acetyl-CoA to promote p65 acetylation-dependent NF-κB activation and antigen presentation. Finally, we detected CD40[+]MHC-II[+]LD[+] astrocytes in multiple sclerosis samples by single-nucleus RNA sequencing and immunohistochemistry. In summary, these studies define a previously unrecognized mechanism by which astrocytes promote CNS autoimmunity.},
}

Animals
*Astrocytes/immunology/metabolism/cytology
*CD40 Antigens/immunology/metabolism
Encephalomyelitis, Autoimmune, Experimental/immunology/pathology
*Autoimmunity/immunology
Mice
Female
*Antigen Presentation/immunology
CD40 Ligand/metabolism/immunology
*Central Nervous System/immunology/cytology
CD4-Positive T-Lymphocytes/immunology
*Histocompatibility Antigens Class II/immunology/metabolism
Th17 Cells/immunology
Humans
Male
Multiple Sclerosis/immunology/pathology
Coculture Techniques
Mice, Inbred C57BL
CRISPR-Cas Systems

@article {pmid42723509,
year = {2026},
author = {Tsuda, H},
title = {Whole-genome safety assessment of Loigolactobacillus coryniformis WBB05 and identification of a candidate gene for aerobic reuterin production.},
journal = {The Journal of dairy research},
volume = {},
number = {},
pages = {1-7},
doi = {10.1017/S0022029926102659},
pmid = {42723509},
issn = {1469-7629},
abstract = {This study reports on the safety profile of Loigolactobacillus coryniformis WBB05 for food industry applications and identifies glycerol-3-phosphate oxidase (GlpO) as a candidate gene associated with aerobic reuterin production. The safety of L. coryniformis WBB05 was evaluated through whole-genome sequencing, phenotypic analysis of haemolytic activity and determination of minimum inhibitory concentrations (MICs) of antibiotics. Comparative genomic analysis was performed to identify candidate genetic determinants for aerobic reuterin production. The draft genome (2.83 Mb, 179 contigs) harboured no known virulence factors, acquired antimicrobial resistance (AMR) genes or biogenic amine biosynthetic genes. Prophage analysis identified only one incomplete prophage region, and four CRISPR-Cas systems (212 spacers) were consistent with phage defence capacity. Secondary metabolite analysis revealed biosynthetic gene clusters encoding a coagulin-like bacteriocin. No β-haemolytic activity was observed. The MICs of all antibiotics tested were below the European Food Safety Authority cut-off values except for kanamycin (128 mg/L), although no acquired AMR genes were detected. Comparative genomic analysis revealed that L. coryniformis WBB05 possesses two putative copies of GlpO, a gene not detected in publicly available genomes of Limosilactobacillus reuteri, which produces reuterin only under anaerobic conditions. These findings support the use of L. coryniformis WBB05 as a safe adjunct culture for dairy applications and highlight GlpO as a candidate determinant of aerobic reuterin production. Further studies comparing GlpO-positive and GlpO-negative strains under aerobic and anaerobic conditions are warranted to confirm the role of GlpO.},
}

@article {pmid42725110,
year = {2026},
author = {Nilova, O and Zajakina, A},
title = {Next-generation macrophage engineering in cancer therapy: From TAM reprogramming to CAR-macrophages.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {3},
pages = {103060},
pmid = {42725110},
issn = {2162-2531},
abstract = {Macrophages are central regulators of the tumor microenvironment (TME), shaping immune suppression, angiogenesis, metabolism, and therapeutic resistance in solid cancers. While early strategies sought to deplete tumor-associated macrophages (TAMs) or block monocyte recruitment, limited efficacy and compensatory mechanisms revealed the need for functional reprogramming rather than elimination. Recent advances in viral vectors, CRISPR-Cas genome editing, and RNA-based delivery platforms have enabled precise genetic modification of macrophages, giving rise to chimeric antigen receptor macrophages (CAR-Ms) and related engineered products. Beyond antigen targeting, effective macrophage engineering requires stabilization of pro-inflammatory identity, resistance to tumor-induced repolarization, metabolic reinforcement, and integration of checkpoint modulation pathways. This review synthesizes current strategies across DNA, mRNA, and siRNA-based platforms, highlighting convergent design principles that connect TAM reprogramming with CAR-M development. We discuss reshaping phagocytosis checkpoints, metabolic and transcriptional stabilization, cytokine augmentation, and synthetic receptor architecture, emphasizing combinatorial and context-aware engineering, while proposing new candidate gene targets. Engineered macrophages are thus evolving from simple effector cells into programmable immune coordinators capable of converting immunologically "cold" tumors into inflamed, therapy-responsive niches.},
}

@article {pmid42725430,
year = {2026},
author = {Ding, W and Yang, X and Yang, Y and Liu, M and Liu, C and Wang, J and Liu, X},
title = {Repeat region engineering of Cas13a crRNA enables conformational gating-based autocatalytic CRISPR biosensing.},
journal = {Nucleic acids research},
volume = {54},
number = {17},
pages = {},
pmid = {42725430},
issn = {1362-4962},
support = {22474111//National Natural Science Foundation of China/ ; 22104077//National Natural Science Foundation of China/ ; 2026JC-YXQN-058//Natural Science Basic Research Program/ ; 2025RS-CXTD-058//Innovation Capability Support Program/ ; 25ZQRC00009//Xi'an Science and Technology Project/ ; //Northwest A&F University/ ; },
mesh = {*CRISPR-Associated Proteins/genetics/metabolism/chemistry ; *Biosensing Techniques/methods ; *CRISPR-Cas Systems ; *Repetitive Sequences, Nucleic Acid ; Nucleic Acid Conformation ; *Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {CrRNA engineering has emerged as a pivotal strategy for extending CRISPR-Cas13a biosensing. However, structural modulation of the direct repeat (DR) region remains exceptionally challenging due to its intricate architecture and the high energetic barrier of the Cas13a-crRNA interface, which is conventionally viewed as a rigid and immutable scaffold. Here, we demonstrate that the DR region is instead a programmable topological element with unexpected structural plasticity. By systematically engineering the DR through sequence insertion and structural splitting, we identified multiple DR variants that retain robust catalytic activity. Crucially, this topological reconfiguration enables Cas13a activity to be precisely gated by unmodified nucleic acid blockers, a level of regulation unattainable with the wild-type crRNA. Building on this flexible modulation, we developed Dre-CRISPR, a DR-engineered platform that couples target-triggered DR restoration to a self-reinforcing autocatalytic loop. This self-amplifying system provides a 2 × 106-fold sensitivity enhancement over nonamplified systems. Furthermore, the Dre-CRISPR platform extends the diagnostic scope of Cas13a to a broader spectrum of analytes, ranging from microRNAs to enzymatic activities and heavy metal ions. Our findings redefine the crRNA scaffold as a versatile signaling node and provide a generalizable framework for developing high-sensitivity, self-amplifying CRISPR biosensors through topology-driven guide RNA engineering.},
}

*CRISPR-Associated Proteins/genetics/metabolism/chemistry
*Biosensing Techniques/methods
*CRISPR-Cas Systems
*Repetitive Sequences, Nucleic Acid
Nucleic Acid Conformation
*Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid42725481,
year = {2026},
author = {Li, Z and Li, F and Jiang, X},
title = {Confinement-enabled nanobiosensing: from chemical signal amplification to programmable single-molecule diagnostics.},
journal = {Chemical communications (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6cc04236h},
pmid = {42725481},
issn = {1364-548X},
abstract = {For rare targets in complex samples, ultrasensitive biosensing requires not only strong signal amplification but also reliable discrimination of target-derived signals from the background. Confinement-enabled nanobiosensing addresses this challenge by organizing molecular recognition, amplification and readout across nanoscale interfaces and microscale compartments. In this Feature Article, we review how chemical amplification strategies, from plasmonic nanogold probes and enzyme-triggered cascades to CRISPR-Cas signal networks, are being coupled with droplets and microwell arrays to convert ensemble signals into digital molecular counts. We further highlight programmable microfluidics, particularly digital microfluidics, as an automation layer for sample handling, washing, reagent exchange and compartment sealing. Recent dual-digital immunoassay platforms illustrate how fluidic digitization and molecular digitization can be integrated for single-molecule diagnostics. We conclude by outlining challenges in interface stability, scalable fabrication, multiplexed readout and clinical translation.},
}

@article {pmid42725609,
year = {2026},
author = {Meka, SG and A, SS and Dasari, V and Ali, OAI and Yeddhu, Y and Kuragala, N and Gudisinti, V and E, B},
title = {Nanocarrier-enabled Gene and Nucleic Acid Therapeutics for Rheumatoid Arthritis: Advances, Translational Evidence, and Regulatory Challenges.},
journal = {Recent advances in inflammation & allergy drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127722708482830260826121447},
pmid = {42725609},
issn = {2772-2716},
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovial inflammation, cartilage degradation, and bone erosion. Conventional diseasemodifying antirheumatic drugs and biologics, although effective in many patients, are limited by systemic toxicity, variable responsiveness, and loss of efficacy over time. Recent advances in nanomedicine have enabled the development of non-viral and viral gene delivery platforms designed to modulate pathogenic pathways at the molecular level. Non-viral nanocarriers, including liposomes, polymeric nanoparticles, lipid nanoparticles, and hybrid systems, have demonstrated efficient delivery of siRNA, antisense oligonucleotides, and mRNA targeting key inflammatory mediators such as TNF-α and NF-κB, resulting in significant disease attenuation in preclinical RA models. Viral vectors, particularly adeno-associated viruses and lentiviruses, provide sustained intra-articular gene expression but raise concerns related to immunogenicity and long-term safety. Emerging gene-editing strategies, notably CRISPR/Cas-based approaches, offer the potential to precisely and durably modulate disease-driving genes. But clinical translation is restricted by off-target effects, ethical considerations, and regulatory barriers. Collectively, the available evidence underscores both the therapeutic potential and inherent complexity of nanocarrier-mediated gene and nucleic acid therapies for RA, emphasizing the necessity for optimized delivery strategies, rigorous safety assessments, and biomarker-guided patient stratification to achieve successful clinical translation. This review comprehensively covered various gene delivery modalities, including non-viral and viral vectors, and gene editing (CRISPR/Cas) approaches. At the end, preclinical and clinical evidence, along with extensive case studies, for RA treatment were also highlighted. This review also outlined challenges and future directions in the management of arthritis.},
}

@article {pmid41152569,
year = {2026},
author = {Whittaker, MN and Testa, LC and Quigley, A and Brooks, DL and Grandinette, SA and Said, H and Dwivedi, G and Jindal, I and Volpp, D and Hacker, JL and Qu, P and Wang, JZ and Levine, MA and Ahrens-Nicklas, RC and Li, Q and Musunuru, K and Alameh, MG and Peranteau, WH and Wang, X},
title = {Improved specificity and efficiency of in vivo adenine base editing therapies with hybrid guide RNAs.},
journal = {Nature biomedical engineering},
volume = {10},
number = {9},
pages = {1943-1955},
pmid = {41152569},
issn = {2157-846X},
support = {Predoctoral Fellowship//American Heart Association (American Heart Association, Inc.)/ ; R01-HD110733//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Graduate Research Fellowship//National Science Foundation (NSF)/ ; U19 NS132301/NS/NINDS NIH HHS/United States ; U01-TR005355//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 HD110733/HD/NICHD NIH HHS/United States ; R21-AR084212//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Career Development Award//American Heart Association (American Heart Association, Inc.)/ ; U19-NS132301//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Animals ; *Adenine/metabolism ; Mice ; *RNA, Guide, CRISPR-Cas Systems/genetics ; Tyrosinemias/genetics/therapy ; *Genetic Therapy/methods ; },
abstract = {Phenylketonuria (PKU), pseudoxanthoma elasticum (PXE) and hereditary tyrosinemia type 1 (HT1) are autosomal recessive disorders linked to the PAH, ABCC6, and FAH and HPD genes, respectively. Here we evaluate the off-target editing profiles of clinical lead guide RNAs (gRNAs) that, when combined with adenine base editors (ABEs), correct the recurrent PAH P281L variant, PAH R408W variant or ABCC6 R1164X variant, or disrupt either of two sites in the HPD gene (a modifier gene of HT1) in human hepatocytes. To mitigate off-target mutagenesis, we systematically screen hybrid gRNAs with DNA nucleotide substitutions. Comprehensive and variant-aware specificity profiling of these hybrid gRNAs reveals dramatically reduced off-target editing and reduced bystander editing in cells. In humanized PAH P281L and ABCC6 R1164X mouse models of PKU and PXE, we show that when formulated in lipid nanoparticles with ABE messenger RNA, selected hybrid gRNAs revert disease phenotypes, reduce off-target editing, increase on-target editing and reduce bystander editing in vivo. These studies highlight the use of hybrid gRNAs to improve the safety and efficiency of adenine base-editing therapies.},
}

Humans
Animals
*Adenine/metabolism
Mice
*RNA, Guide, CRISPR-Cas Systems/genetics
Tyrosinemias/genetics/therapy
*Genetic Therapy/methods

@article {pmid42336896,
year = {2026},
author = {Novoa, JJ and Gaykema, LH and de Klerk, JA and Peerlings, JHD and van Nieuwland, RY and van der Slik, A and van den Hil, FE and Orlova, VV and Gonçalves, MAFV and van den Berg, CW and Rabelink, TJ and Zaldumbide, A},
title = {CRISPR-Cas9-mediated knock-in of cytomegalovirus US2 provides an alternative strategy for generating hypoimmunogenic hiPSC lines.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42336896},
issn = {2045-2322},
support = {2020-01//LUF/Stichting Prof. Jaap de Graeff-Lingling Wiyadharma Fonds/ ; NNF21CC0073729//Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW)/ ; },
mesh = {Humans ; *Cytomegalovirus/genetics ; *CRISPR-Cas Systems ; HLA-A2 Antigen/immunology/genetics/metabolism ; *Induced Pluripotent Stem Cells/immunology/metabolism/cytology ; Killer Cells, Natural/immunology ; *Viral Proteins/genetics ; Cell Line ; T-Lymphocytes/immunology ; Lymphocyte Activation ; Viral Envelope Proteins ; },
abstract = {Mismatches in HLA haplotypes between donors and recipients significantly increase the risk of graft failure due to immune rejection. Knockout (KO) of beta-2 microglobulin (B2M) is the current standard for eliminating HLA class I (HLA-I) surface expression and protecting allogeneic products from T-cell-mediated rejection; however, complete HLA-I ablation can trigger natural killer (NK) cell "missing-self" responses and disrupt critical immune-regulatory interactions. To address these limitations, we introduced a cytomegalovirus-derived US2 encoding sequence into the AAVS1 safe-harbor locus of a human induced pluripotent stem cell (hiPSC) line. Flow cytometry showed that US2 selectively abrogates HLA-A2 surface expression while retaining low levels of total HLA-I. In coculture assays, US2 expression abolished HLA-A2 alloreactive T-cell activation without increasing NK cell degranulation, indicating preserved inhibitory signaling. Together, these findings establish US2-mediated immune evasion as a refined single-edit alternative to B2M KO, enabling selective HLA-I modulation while preserving critical immune-regulatory interactions.},
}

Humans
*Cytomegalovirus/genetics
*CRISPR-Cas Systems
HLA-A2 Antigen/immunology/genetics/metabolism
*Induced Pluripotent Stem Cells/immunology/metabolism/cytology
Killer Cells, Natural/immunology
*Viral Proteins/genetics
Cell Line
T-Lymphocytes/immunology
Lymphocyte Activation
Viral Envelope Proteins

@article {pmid42544503,
year = {2026},
author = {Zou, G and Xie, J and Wu, M and Wei, X and Li, J},
title = {An electrochemiluminescence biosensor for sulfadimethoxine detection based on enzymatic DNA walker-activated CRISPR/Cas12a cascade for signal enhancement.},
journal = {The Analyst},
volume = {151},
number = {18},
pages = {5335-5343},
doi = {10.1039/d6an00344c},
pmid = {42544503},
issn = {1364-5528},
mesh = {*Biosensing Techniques/methods ; *Sulfadimethoxine/analysis ; Luminescent Measurements/methods ; *Electrochemical Techniques/methods ; *CRISPR-Cas Systems ; *DNA/chemistry/genetics ; Limit of Detection ; Gold/chemistry ; Aptamers, Nucleotide/chemistry/genetics ; Electrodes ; Ferrous Compounds/chemistry ; Metallocenes/chemistry ; },
abstract = {Sulfadimethoxine (SDM) is a widely used veterinary antibiotic. Its residues in food and the environment may cause bacterial resistance and threaten human health. In this study, a novel electrochemiluminescence (ECL) biosensor with signal amplification was developed for the sensitive detection of SDM. A g-C3N4@Au composite was modified on the electrode surface, generating a strong ECL signal with K2S2O8 as the coreactant. Hairpin DNA terminated with ferrocene carboxylic acid (FcA) was self-assembled onto g-C3N4@Au via thiol-gold bonds, causing Fc to quench the electrochemiluminescence signal of g-C3N4. Upon SDM addition, it specifically bound to the aptamer strand, releasing the DNA Walker. The DNA walker then continuously hybridized with the activator strand S1 and was cleaved by the nicking endonuclease Nt.BsmAI, generating a large number of S1. S1 further activated the trans-cleavage activity of CRISPR/Cas12a, which cleaves the hairpin DNA on the electrode, releasing Fc and recovering the ECL signal. By monitoring the ECL intensity change during the "signal-off" to "signal-on" transition, quantitative detection of SDM was indirectly realized. The detection range for SDM is 1.0 × 10[-14] to 1.0 × 10[-7] mol L[-1], with a detection limit of 7.15 × 10[-15] mol L[-1]. The sensor was successfully applied to the detection of SDM in food and water samples. Benefiting from the catalytic cascade amplification involving multiple enzymes, the developed method demonstrated high ultrahigh sensitivity.},
}

*Biosensing Techniques/methods
*Sulfadimethoxine/analysis
Luminescent Measurements/methods
*Electrochemical Techniques/methods
*CRISPR-Cas Systems
*DNA/chemistry/genetics
Limit of Detection
Gold/chemistry
Aptamers, Nucleotide/chemistry/genetics
Electrodes
Ferrous Compounds/chemistry
Metallocenes/chemistry

@article {pmid42601452,
year = {2026},
author = {Pecori, R and Casati, B and Merdler-Rabinowicz, R and Landesman, N and Sanghvi, K and Zens, S and Bilgin, E and Topouzi, M and Kipfstuhl, K and Pinamonti, V and Arnold, A and Abukhalaf, M and Gomez-Zepeda, D and Tenzer, S and Lindner, JM and Platten, M and Offringa, R and Carretero, R and Ruppin, E and Levanon, EY and Papavasiliou, FN},
title = {Engineering editopes through programmable RNA editing toward tumor neoantigen generation.},
journal = {The EMBO journal},
volume = {45},
number = {18},
pages = {6655-6678},
pmid = {42601452},
issn = {1460-2075},
support = {2039/20 and 231/21//Israel Science Foundation (ISF)/ ; 2021//HI-TRON seed funding program 2021/ ; 439669440 TRR319 RMaP TP A04//Deutsche Forschungsgemeinschaft (DFG)/ ; Project "ENIGMA"//DKFZ-Hector Seed Funding/ ; Core Funding DKFZ//Helmholtz Association ()/ ; },
mesh = {*RNA Editing ; Humans ; Animals ; Adenosine Deaminase/genetics/metabolism ; *Antigens, Neoplasm/immunology/genetics ; RNA-Binding Proteins/genetics/metabolism ; Mice ; MART-1 Antigen/immunology/genetics ; Cell Line, Tumor ; Immunotherapy/methods ; *Epitopes/immunology/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; *Neoplasms/immunology/genetics/therapy ; T-Lymphocytes/immunology ; },
abstract = {Neoepitope-based therapies hold great promise for cancer immunotherapy because they target tumor-specific mutations and elicit potent anti-tumor T-cell responses. However, their clinical implementation remains limited by the complexity of neoepitope discovery and uncertainty regarding presentation by tumor cells. A potential alternative is the generation of immunogenic neoepitopes directly within cancer cells through programmable RNA editing. Here, we develop Short Precise-Encodable ADAR Recruiting (SPEAR) gRNAs that harness endogenous ADAR1 to direct precise adenosine-to-inosine (A-to-I) editing at selected transcript sites. Using these gRNAs, we demonstrate the generation of immunogenic neoepitopes through RNA editing at the transcript level, termed editopes. In a proof-of-concept model based on the melanoma antigen MART-1, SPEAR-mediated RNA editing restored antigen-specific T cell recognition and enabled tumor control in vivo. Finally, we developed a computational pipeline to identify candidate tumor-selective neoepitopes across multiple cancer types amenable to guided RNA editing. Our findings establish programmable RNA editing as a strategy for engineering immunogenic editopes and provide a framework for neoepitope-directed cancer immunotherapy.},
}

*RNA Editing
Humans
Animals
Adenosine Deaminase/genetics/metabolism
*Antigens, Neoplasm/immunology/genetics
RNA-Binding Proteins/genetics/metabolism
Mice
MART-1 Antigen/immunology/genetics
Cell Line, Tumor
Immunotherapy/methods
*Epitopes/immunology/genetics
RNA, Guide, CRISPR-Cas Systems/genetics
*Neoplasms/immunology/genetics/therapy
T-Lymphocytes/immunology

@article {pmid42657609,
year = {2026},
author = {Lin, X and Ye, P and Ding, Y and Cao, Y and Wang, Y and He, J and Zhou, Y},
title = {A cascaded CHA-CRISPR/Cas12a photoelectrochemical platform enabled by S-scheme Bi2WO6/BiOBr for piR-823 detection.},
journal = {The Analyst},
volume = {151},
number = {18},
pages = {5510-5517},
doi = {10.1039/d6an00974c},
pmid = {42657609},
issn = {1364-5528},
mesh = {Bismuth/chemistry ; *Electrochemical Techniques/methods ; *CRISPR-Cas Systems/genetics ; Humans ; *Biosensing Techniques/methods ; Limit of Detection ; *RNA, Small Interfering/analysis/genetics ; Tungsten Compounds/chemistry ; Exosomes/chemistry ; Photochemical Processes ; *Biomarkers, Tumor/analysis ; },
abstract = {Exosomal piR-823 is a promising specific biomarker for colorectal cancer, yet its ultrasensitive detection remains challenging due to its extremely low abundance and high sequence complexity. Herein, we developed a cascaded CHA-CRISPR/Cas12a photoelectrochemical (PEC) sensing platform enabled by an S-scheme Bi2WO6/BiOBr heterojunction for the reliable detection of piR-823. The flower-like spherical Bi2WO6/BiOBr heterojunction exhibits enhanced visible-light absorption and efficient charge transfer arising from the S-scheme structure, which establishes a strong photoactive basis for the PEC platform. By integrating catalytic hairpin assembly with CRISPR/Cas12a trans-cleavage activity, a cascaded signal amplification strategy is established, which significantly improves the detection sensitivity. Under optimized conditions, the platform shows a distinct negative correlation between transient photocurrent and the logarithm of piR-823 concentration (1.0-1.0 × 10[6] fM), with an ultralow detection limit of 0.34 fM (S/N = 3). It also demonstrates high specificity, good reproducibility, and satisfactory recovery (96.87%-103.41%) in exosome lysate. This work not only presents an efficient PEC biosensing platform for piRNA analysis but also offers guidance for the rational construction of S-scheme heterojunctions in high-performance PEC biosensors, holding great promise for early colorectal cancer diagnosis and prognostic monitoring.},
}

Bismuth/chemistry
*Electrochemical Techniques/methods
*CRISPR-Cas Systems/genetics
Humans
*Biosensing Techniques/methods
Limit of Detection
*RNA, Small Interfering/analysis/genetics
Tungsten Compounds/chemistry
Exosomes/chemistry
Photochemical Processes
*Biomarkers, Tumor/analysis

@article {pmid42677820,
year = {2026},
author = {Chen, J and He, M and Yin, F and Pan, H and Chao, M and Cheng, W and Sun, H and Wang, Z and Xiang, Y},
title = {A rapid and straightforward detection of the novel obesity gene LGR4 A750T point mutation by the single-tube Cas12a system with split crRNA.},
journal = {Journal of materials chemistry. B},
volume = {14},
number = {35},
pages = {11039-11045},
doi = {10.1039/d6tb01366j},
pmid = {42677820},
issn = {2050-7518},
mesh = {*Point Mutation/genetics ; Humans ; *Receptors, G-Protein-Coupled/genetics ; *Obesity/genetics ; *CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {With the increasing number of obesity cases globally, immediate screening for obesity-related mutations has become increasingly important. LGR4 is a novel obesity gene. Here, we report a dual-mode detection strategy for the LGR4 p.A750T genetic variant by integrating asymmetric recombinase polymerase amplification (aRPA) with a split CRISPR-Cas12a system. Through isothermal aRPA amplification, the system directly generates abundant single-stranded DNA products that activate the split Cas12a complex, enabling ultra-sensitive and PAM-independent detection without spatial constraints on mutation sites. By employing a split crRNA design rather than conventional CRISPR-Cas12a, the method demonstrates exceptional specificity in distinguishing DNA point mutations. The assay achieves a detection limit of 13.5 fM, exhibits excellent linearity from 100 fM to 1 nM, and completes analysis within 30 minutes. Furthermore, when coupled with lateral flow test strip visualization, the system eliminates the need for sophisticated instrumentation and enables rapid single-tube amplification for interpretation of results. Based on the high mutation discrimination capability of the SCas12a system, the method achieves highly sensitive and specific LGR4 point mutation detection.},
}

*Point Mutation/genetics
Humans
*Receptors, G-Protein-Coupled/genetics
*Obesity/genetics
*CRISPR-Cas Systems/genetics
Nucleic Acid Amplification Techniques/methods

@article {pmid42716490,
year = {2026},
author = {Qu, Y and Wang, Y and Wang, Y and Tang, H and Chen, Q},
title = {SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42716490},
issn = {1477-4054},
support = {32572957//National Natural Science Foundation of China/ ; },
mesh = {*CRISPR-Cas Systems ; *Software ; Humans ; Algorithms ; *RNA, Guide, CRISPR-Cas Systems/genetics ; Genome, Plant ; Genomics/methods ; Computational Biology/methods ; },
abstract = {The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.},
}

*CRISPR-Cas Systems
*Software
Humans
Algorithms
*RNA, Guide, CRISPR-Cas Systems/genetics
Genome, Plant
Genomics/methods
Computational Biology/methods

@article {pmid42716927,
year = {2026},
author = {Cong, T and Xu, R and Chen, X and Yuan, J and Lin, Z and Yang, W and Ju, A and Wang, L and Wang, Q and Zhang, J and Li, Y and Li, D and Zhu, M},
title = {Ultra-sensitive profiling of CRISPR-Cas off-target effects with Tracking-seq2.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42716927},
issn = {2041-1723},
support = {32571678//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82322054//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)/ ; },
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Gene Editing/methods ; Hematopoietic Stem Cells/metabolism ; T-Lymphocytes/metabolism ; DNA End-Joining Repair ; },
abstract = {Accurate detection of off-target activity in primary human cells is crucial for ensuring the safety of gene therapies, yet existing methods often lack sufficient sensitivity. To address this limitation, we develop Tracking-seq2, an advanced technology that integrates exogenous 5' → 3' exonuclease treatment and non-homologous end joining (NHEJ) pathway inhibitors with the original Tracking-seq. Tracking-seq2 exhibits enhanced sensitivity in profiling off-target sites of diverse genome editors-including Cas9, Cas12a, cytosine base editors (CBEs), adenine base editors (ABEs), and prime editors (PEs). Critically, Tracking-seq2 is directly applicable to clinically relevant primary human cell types, such as T cells and CD34[+] hematopoietic stem and progenitor cells (HSPCs). Furthermore, our findings reveal that genomic variations drive distinct off-target heterogeneity across different individuals, highlighting the necessity for personalized safety assessment in clinical genome editing applications. Tracking-seq2 provides a robust platform for sensitive off-target detection in primary cells, with sensitivity comparable to or exceeding current state-of-the-art methods.},
}

Humans
*CRISPR-Cas Systems/genetics
*Gene Editing/methods
Hematopoietic Stem Cells/metabolism
T-Lymphocytes/metabolism
DNA End-Joining Repair

@article {pmid42717063,
year = {2026},
author = {Ocampo, RF and Orosco, C and Huang, B and West, MS and Parker, B and Jain, PK and Taylor, DW},
title = {Architecture of a DNA-guided Cas12a.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
pmid = {42717063},
issn = {1545-9985},
abstract = {CRISPR-Cas systems have largely been restricted to RNA-guided nucleases. Here, we present the cryo-electron microscopy structure of Acidaminococcus sp. Cas12a bound to a pseudo-DNA (ΨDNA) guide and RNA target, revealing how Cas12a can accomplish DNA-guided RNA recognition. The ΨDNA hairpin bridges the recognition and nuclease lobes, mimicking a PAM-proximal duplex and positioning the spacer to allow formation of a canonical RNA-DNA heteroduplex along the recognition lobe. This provides a structural framework for its activity and provides a potential blueprint for future engineering.},
}

@article {pmid42717197,
year = {2026},
author = {Zhang, H and Luo, S and Wang, X and Lin, L and Liang, R and Zhong, C and Zhang, Y and Zhao, W and Chen, Z and Liu, X and Gao, Y and Chen, F and Sun, N and Huang, J and Fei, T},
title = {Towards efficient perturbation for the noncoding genome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42717197},
issn = {2041-1723},
support = {32470673//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {CRISPR-Cas Systems/genetics ; *RNA, Untranslated/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; *Genome ; Humans ; Animals ; CRISPR-Associated Protein 9/metabolism/genetics ; *Gene Editing/methods ; },
abstract = {Deciphering the functionality of the noncoding genome, which includes important cis-regulatory elements (CREs) and transcribed noncoding RNA genes, remains technically challenging. Here, using massively parallel genetic screening, we systematically benchmark the performance of five representative loss-of-function perturbation tools, including single-guide RNA (gRNA) mediated SpCas9 cleavage or CRISPR interference, and paired gRNA (pgRNA) involved dual-SpCas9, Big Papi (paired SpCas9 and SaCas9) or dual-enAsCas12a fragment deletion methods, in decoding the roles of the noncoding genome. For targeting CREs such as enhancers, dual-SpCas9 outperforms other methods with superior efficiency in destroying functional genomic regions. For perturbing noncoding RNA genes, in addition to dual-SpCas9, other RNA-targeting methods such as RNA interference are recommended to discriminate transcript-dependent or -independent roles. A deep learning model, DeepDC, with an associated web server, is built to facilitate optimal dual-SpCas9 pgRNA design for efficiently deleting a genomic fragment. Together, our work provides practical guidance on selecting appropriate loss-of-function tools to resolve the functional complexity of the noncoding genome.},
}

CRISPR-Cas Systems/genetics
*RNA, Untranslated/genetics
RNA, Guide, CRISPR-Cas Systems/genetics
*Genome
Humans
Animals
CRISPR-Associated Protein 9/metabolism/genetics
*Gene Editing/methods

@article {pmid42720682,
year = {2026},
author = {Ullah, I and Ahmad, N and Bhat, AH and Hussain, A and Wei, F and Hongzhi, W},
title = {Engineering cold stress resilience in capsicum annuum through functional genomics and precision breeding.},
journal = {Plant cell reports},
volume = {45},
number = {10},
pages = {},
pmid = {42720682},
issn = {1432-203X},
mesh = {*Capsicum/genetics/physiology ; *Genomics/methods ; *Plant Breeding/methods ; Gene Expression Regulation, Plant/genetics ; *Cold-Shock Response/genetics/physiology ; Cold Temperature ; },
abstract = {This review synthesizes the molecular mechanisms of cold tolerance in pepper, integrating multi-omics data,genome editing, and precision breeding strategies to accelerate the development of cold-resilient cultivars. Cold stress is a significant environmental factor that affects the growth, productivity, and fruit quality of Capsicum annuum by impairing membrane integrity photosynthesis and cellular redox homeostasis. Although pepper has several endogenous cold-responsive regulators such as CaNAC035 and CabHLH035, along with antioxidant defense systems, its cold tolerance remains limited due to low transcriptional activation of key regulators, functional redundancy among cold-responsive genes, and the polygenicity of cold tolerance. These complexities, combined with low genetic diversity and linkage drag, have hindered the improvement of cold-resistant cultivars through conventional breeding. This review brings together the recent progress in understanding the molecular mechanisms of cold stress perception, signal transduction, transcriptional regulation, metabolic reprogramming, and phytohormone interactions in pepper. Precision Breeding 2.0 is a new innovation that combines the integration of multi-omics-based target identification with next-generation genome-editing techniques, allowing precise and multiplex engineering of complex and interconnected regulatory networks instead of single genes. We cover new approaches such as engineering the DREB/CBF pathway, allele-specific editing and targeted disruption of negative regulators to enhance the pathway(s) involved in cold response. Moreover, we propose a roadmap for integration of transcriptomics, proteomics, metabolomics, high-throughput phenomics, and speed breeding to accelerate the identification, validation, and deployment of superior alleles to boost cold tolerance. This review provides a foundation for developing climate-resilient pepper cultivars by connecting functional genomics with precision genome engineering approaches to maintain productivity under variable environmental conditions.},
}

*Capsicum/genetics/physiology
*Genomics/methods
*Plant Breeding/methods
Gene Expression Regulation, Plant/genetics
*Cold-Shock Response/genetics/physiology
Cold Temperature

@article {pmid42720869,
year = {2026},
author = {Lu, D and Li, Z and Zhu, P and Zhang, Z and Liu, P and Meng, L and Sun, X and Yang, Q and Song, J and Li, Z},
title = {Development and evaluation of a single-tube RT-ERA-CRISPR/Cas12a assay for simultaneous detection of enterovirus G and recombinant strains with papain-like cysteine protease gene insertion.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42720869},
issn = {1573-7446},
support = {202304BI090001//Project of Innovation Guide and S&T Enterprise Cultivation of Yunnan Province/ ; 202102AE090039//Major Science and Technology Project of Yunnan Province/ ; 202401AS070010//Applied Basic Research Foundation of Yunnan Province/ ; YNWR-QNBJ-2020-211//Ten Thousand Talent Plans for Youth Top-notch Talents of Yunnan Province/ ; },
mesh = {Animals ; *Swine Diseases/virology/diagnosis ; Swine ; *CRISPR-Cas Systems ; *Enterovirus Infections/veterinary/diagnosis/virology ; Nucleic Acid Amplification Techniques/veterinary/methods ; Sensitivity and Specificity ; *Cysteine Proteases/genetics ; *Enteroviruses, Porcine/genetics/isolation & purification ; Diarrhea/veterinary/virology/diagnosis ; Feces/virology ; Rapid Diagnostic Tests ; },
abstract = {Enterovirus G (EV-G) strains carrying the papain-like cysteine protease (PLCP) gene insertion have recently emerged as important pathogens associated with diarrhea in weaned piglets. Herein, a single-tube reverse transcription-enzymatic recombinase amplification coupled with CRISPR/Cas12a (RT-ERA-CRISPR/Cas12a) dual-readout assay was established to concurrently detect pan-EV-G via conserved RNA-dependent RNA polymerase 3D-encoding gene and screen pathogenic PLCP-carrying recombinant strains. After systematic optimization of primer-probe set and reaction parameters, the analytical and clinical performances of the established assay were evaluated. The assay exhibited no cross-reaction with other common porcine diarrhea-associated viruses or closely related members of the Picornaviridae family. Its limits of detection reached 5.19 copies·µL[-1] for the 3D-encoding gene and 5.51 copies·µL[-1] for the PLCP gene, demonstrating superior sensitivity compared with conventional RT-PCR, RT-qPCR, RPA, and LAMP assays. Testing 96 field fecal samples yielded almost perfect agreement with RT-qPCR (κ = 0.95, concordance = 97.92%) and moderate consistency with conventional RT-PCR (κ = 0.68, concordance = 87.88%), respectively. Unlike multiplex CRISPR-Cas12a platforms that suffer from reporters' interference from Cas12a non-specific cleavage and dual nfo-probe systems prone to oligonucleotide dimerization, this work implemented separated visual readouts: nfo-probe lateral flow strips for 3D-encoding gene amplicons and Cas12a collateral cleavage for PLCP gene amplification products. An 85 ℃ heating step neutralized endonuclease Ⅳ to remove potential CRISPR signal inhibition, realizing unified single-tube detection. This assay is rapid, cost-efficient, and features high specificity and sensitivity. It offers a practical on-farm surveillance tool for virulent PLCP-recombinant EV-G, facilitating prevention and control of swine diarrheal diseases and safeguarding pork production safety.},
}

Animals
*Swine Diseases/virology/diagnosis
Swine
*CRISPR-Cas Systems
*Enterovirus Infections/veterinary/diagnosis/virology
Nucleic Acid Amplification Techniques/veterinary/methods
Sensitivity and Specificity
*Cysteine Proteases/genetics
*Enteroviruses, Porcine/genetics/isolation & purification
Diarrhea/veterinary/virology/diagnosis
Feces/virology
Rapid Diagnostic Tests

@article {pmid42721033,
year = {2026},
author = {Park, HH},
title = {Diverse routes to Cas3 activation in type I CRISPR-Cas immunity.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117899},
doi = {10.1016/j.celrep.2026.117899},
pmid = {42721033},
issn = {2211-1247},
abstract = {Jiang et al. show that the type I-A CRISPR system of Saccharolobus islandicus recruits Cas3 only after target recognition. Their study reveals different Cas3 activation mechanisms and a dual role of ATP in target degradation and collateral cleavage.},
}

@article {pmid42722935,
year = {2026},
author = {Demir, B and Aydin, EA and Sağlam, A},
title = {Bridging the bench-to-field gap: a quantitative multi-omics and CRISPR/Cas9 framework for climate-resilient agriculture.},
journal = {Transgenic research},
volume = {35},
number = {1},
pages = {},
pmid = {42722935},
issn = {1573-9368},
mesh = {Multiomics ; *CRISPR-Cas Systems/genetics ; *Crops, Agricultural/genetics/growth & development ; *Plants, Genetically Modified/genetics/growth & development ; Climate Change ; Gene Editing ; *Agriculture/methods ; Drought Resistance ; },
abstract = {Global climate change and shrinking freshwater supplies threaten agricultural sustainability. A major translational bottleneck exists: drought-tolerant genotypes developed in labs often fail in open-field conditions due to phenotypic mismatch. Traditional single-gene approaches and static lab tests overlook genotype-by-environment (G × E) interactions, hormonal tradeoffs (involving Abscisic Acid, Jasmonic Acid, Brassinosteroids, and Melatonin), and artificial effects of pots. This review presents an integrated quantitative selection framework to bridge lab and field results. In this review, we propose a conceptual three-stage Predictive Translational Workflow designed to bridge lab and field outcomes by integrating multi-omics envirotyping with advanced mixed models like (G × E)-BLUP and MegaLMM. These methods group complex transcriptomic and metabolomic data into functional networks, filtering out lab artifacts and pinpointing core regulatory nodes stable in real climates. Finally, we show how this pipeline enables precise CRISPR/Cas9 editing of native promoters, reducing agronomic yield penalties in normal conditions and offering a streamlined, non-GMO path to field-resilient crops.},
}

Multiomics
*CRISPR-Cas Systems/genetics
*Crops, Agricultural/genetics/growth & development
*Plants, Genetically Modified/genetics/growth & development
Climate Change
Gene Editing
*Agriculture/methods
Drought Resistance

@article {pmid42141726,
year = {2026},
author = {Dong, J and Zhang, K and Song, M and Xiao, M and Lu, X and Ge, S and Zheng, Z and Li, M and Zhu, JK and Lei, M},
title = {CRISPR-mediated intronic knock-in of pre-amiRNA enables targeted gene silencing.},
journal = {Plant communications},
volume = {7},
number = {9},
pages = {101916},
doi = {10.1016/j.xplc.2026.101916},
pmid = {42141726},
issn = {2590-3462},
mesh = {*Introns/genetics ; *Gene Silencing ; *MicroRNAs/genetics ; Plants, Genetically Modified ; *CRISPR-Cas Systems ; *Gene Knock-In Techniques/methods ; },
abstract = {This study introduces an intronic artificial microRNA (IamiRNA) strategy that combines CRISPR-Cas9-mediated knock-in with endogenous miRNA processing for targeted gene silencing in plants. By inserting amiRNA precursors into introns of endogenous genes, this approach enables effective, tissue-specific gene silencing without persistent transgene expression, offering a promising tool for functional genomics and crop improvement.},
}

*Introns/genetics
*Gene Silencing
*MicroRNAs/genetics
Plants, Genetically Modified
*CRISPR-Cas Systems
*Gene Knock-In Techniques/methods

@article {pmid42319116,
year = {2026},
author = {Qin, Z and Surnido, W and Hozumi, S and Hirano, T and Sawatsubashi, S and Mizuta, H and Uji, T},
title = {Expanding the scope of precision editing in seaweeds through the application of a novel CRISPR-associated nuclease 12a-aligned CRISPR system in Ulva prolifera.},
journal = {Journal of experimental botany},
volume = {77},
number = {17},
pages = {5560-5565},
doi = {10.1093/jxb/erag302},
pmid = {42319116},
issn = {1460-2431},
support = {//Open Innovation Platform with Enterprise, Research Institute and Academia/ ; //Japan Science and Technology Agency/ ; JPJS00420230001//Genome Editing Technology Research Grant, and the JSPS Program for Forming Japan's Peak Research Universities/ ; },
mesh = {*Ulva/genetics ; *CRISPR-Cas Systems ; *Gene Editing/methods ; *Seaweed/genetics ; Edible Seaweeds ; },
abstract = {Seaweeds, such as the fast-growing green alga Ulva prolifera, can be harnessed as valuable marine crops. The lack of scalable genome-editing tools hampers functional genomics to explore and elucidate algal molecular pathways with industrial importance. Here, we expanded precision genome modification in seaweeds by successfully demonstrating gene editing with a transgene-free AT-rich-targeting CRISPR-associated protein (Cas) system in U. prolifera. By evaluating various delivery buffers, comparing different Cas systems, and optimizing incubation temperatures, we determined suitable conditions for more widespread applicability of a novel Cas12a-aligned ST8 editor. We obtained >50 ST8-mediated knockout mutants of a toxin-based endogenous marker gene, UpAPT, at 28 °C post-delivery incubations. Our work diversified the applicable genome-editing tools in seaweeds, advancing algal functional genomics and providing more strategies to precisely target unexplored seaweed resources.},
}

*Ulva/genetics
*CRISPR-Cas Systems
*Gene Editing/methods
*Seaweed/genetics
Edible Seaweeds

@article {pmid42323890,
year = {2026},
author = {Zhang, TL and Chen, MK and Li, YM and Yu, HW and Ye, LD},
title = {A CRISPR-Cas9 Toolkit Enabling Tunable Integration and Transient Homologous Recombination Enhancement in Yarrowia lipolytica.},
journal = {Biotechnology and bioengineering},
volume = {123},
number = {10},
pages = {2643-2654},
pmid = {42323890},
issn = {1097-0290},
support = {32471481//National Natural Science Foundation of China/ ; 226-2025-00043//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Yarrowia/genetics ; *Homologous Recombination/genetics ; *CRISPR-Cas Systems/genetics ; *Gene Editing/methods ; },
abstract = {Although the oleaginous yeast Yarrowia lipolytica is a promising microbial cell factory, its application remains constrained by inefficient homology-directed repair (HDR) and a lack of precise genomic integration tools. To address these limitations, we developed a comprehensive genetic toolkit featuring three synergistic advancements. First, we systematically identified 55 neutral integration sites with tunable expression profiles, enabling stable, position-independent gene integration with predictable transcriptional output across a 12.88-fold dynamic range. Second, we established a dual-readout high-throughput screening platform combining colony morphology analysis with hrGFP fluorescence. This approach accurately measures locus-specific homologous recombination (HR) efficiency while eliminating false positives by dominant non-homologous end joining (NHEJ). Third, we engineered a transient HR enhancement system by fusing the Sae2 exonuclease to Cas9 via a flexible (GGGGS)3 linker. This fusion significantly boosts HR efficiency and surpasses the cleavage activity of unmodified Cas9 without introducing permanent genomic modifications or compromising cellular fitness. Finally, HR efficiency for single-gene integration was increased from 46.5% to 77.5% while the dual-locus editing efficiency reached 64.1% when using 500-bp homology arms, and the engineered strains demonstrated improved genetic stability compared to those with constitutive HR enhancement.},
}

*Yarrowia/genetics
*Homologous Recombination/genetics
*CRISPR-Cas Systems/genetics
*Gene Editing/methods

@article {pmid42325108,
year = {2026},
author = {Guo, Q and Shen, Q and Zhao, L and Zhou, X and Yan, S and Xue, Y and Zheng, Y},
title = {One Plasmid Is All You Need: Genome Editing in Escherichia coli Using Endogenous TnpB and Endogenous Recombination System.},
journal = {Biotechnology and bioengineering},
volume = {123},
number = {10},
pages = {2690-2701},
pmid = {42325108},
issn = {1097-0290},
support = {2022YFC2105400//National Key Research and Development Program of China/ ; },
mesh = {*Escherichia coli/genetics ; *Plasmids/genetics ; *Gene Editing/methods ; *Recombination, Genetic ; *Escherichia coli Proteins/genetics/metabolism ; CRISPR-Cas Systems ; },
abstract = {Escherichia coli (E. coli) is a key workhorse of biotechnology. Commonly used CRISPR-Cas9 systems for E. coli genome editing are complex and impose metabolic stress on the host, creating demand for more streamlined strategies. Recent studies identified the IS605 transposon-associated TnpB as a programmable RNA-guided (ωRNA) DNA endonuclease, prompting us to explore whether endogenous TnpB in E. coli (EcoTnpB) could be harnessed for genome editing. Biochemical and cellular analyses demonstrated that EcoTnpB efficiently cleaves both chromosomal and plasmid DNA at custom-specified sites in a TAM-dependent manner. Interestingly, E. coli possesses an endogenous recombination machinery capable of repairing EcoTnpB-induced DNA double-strand breaks (DSBs), challenging the long-held view that bacteria lack efficient homologous recombination systems. Based on these findings, we established a single-plasmid editing system (SPEED) in which genome editing is achieved by simply providing ωRNA and a homologous recombination template. By utilizing endogenous EcoTnpB together with the host HR pathway, this system enabled inducible and seamless genome editing at multiple genomic loci in BL21 (DE3), with editing efficiencies ranging from approximately 29% to 56%. Our results demonstrate for the first time that endogenous TnpB can be harnessed for genome editing and may hold potential for broader applications, such as species-specific antimicrobial development.},
}

*Escherichia coli/genetics
*Plasmids/genetics
*Gene Editing/methods
*Recombination, Genetic
*Escherichia coli Proteins/genetics/metabolism
CRISPR-Cas Systems

@article {pmid42366734,
year = {2026},
author = {Köse, AM and Ranalli, M and Trivanovic, D and Maslovaric, I},
title = {Minimizing Off-Target Effects of CRISPR-Cas9 With Optimized sgRNA: Evaluation of Efficiency and Specificity in the Tumor Protein 53 (TP53) Region.},
journal = {Biotechnology and bioengineering},
volume = {123},
number = {10},
pages = {2677-2689},
pmid = {42366734},
issn = {1097-0290},
support = {//Ministry of Science, Technological Development, and Innovation of the Republic of Serbia/ ; },
mesh = {*CRISPR-Cas Systems ; *Tumor Suppressor Protein p53/genetics ; *RNA, Guide, CRISPR-Cas Systems/genetics ; Humans ; *Gene Editing/methods ; Machine Learning ; },
abstract = {CRISPR-Cas9 is a widely used genetic tool with therapeutic potential in molecular biology. CRISPR-Cas9 enables precise genome editing by its ability to target specific DNA sequence. After off-target and on-target regions are identified, CRISPR-Cas9 is applied to these regions based on the match between the guide RNA (gRNA) and target DNA sequence. This study points to the off-target impact of mismatches between the gRNA and target DNA on exon regions of the TP53 gene, which are involved in regulating multiple genes and cellular functions. Off-target positions are typically evaluated using scoring methods. In this study, we have used latent class analysis to reveal subclasses of off-target positions. Thus, we have created the levels of off-target positions and evaluated the effects of mismatching positions within these classes using machine learning classifiers. The results revealed that mismatching positions could be categorized into three levels: low, middle, and high off-target positions. We have improved a computational framework to minimize off-target effects and to identify the PAM sequences in the gRNA design. Thus, carefully designed gRNAs will ensure that desired genetic edits are performed and target variants are achieved. This work will avail the future research aimed at optimizing genome editing by customizing CRISPR-Cas9 to target specific protospacer DNA through gRNA.},
}

*CRISPR-Cas Systems
*Tumor Suppressor Protein p53/genetics
*RNA, Guide, CRISPR-Cas Systems/genetics
Humans
*Gene Editing/methods
Machine Learning

@article {pmid42496673,
year = {2026},
author = {Ning, Z and Wang, G},
title = {Context-Dependent Cancer Vulnerabilities: CRISPR Screening under Inflammatory Stress.},
journal = {Cancer research},
volume = {86},
number = {18},
pages = {4457-4459},
doi = {10.1158/0008-5472.CAN-26-3042},
pmid = {42496673},
issn = {1538-7445},
mesh = {Humans ; *Neoplasms/genetics/pathology/metabolism/immunology ; *Inflammation/genetics ; Tumor Microenvironment/genetics ; *CRISPR-Cas Systems ; Animals ; Cytokines/metabolism ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Oxidative Stress ; Signal Transduction ; Stress, Physiological ; },
abstract = {Genome-wide CRISPR screens have systematically identified genes required for cancer cell survival, yet these studies are typically performed under standardized conditions that do not fully recapitulate the physiologic stresses encountered within the tumor microenvironment. In a recent issue of Nature Genetics, Cheruiyot and colleagues perform genome-wide loss-of-function screens under inflammatory conditions induced by interferon (IFN) β, IFNγ, and tumor necrosis factor (TNF), revealing that distinct cytokines impose different genetic requirements for tumor cell survival. The study shows that inflammatory signaling reshapes the genetic dependency landscape in a cytokine-specific manner. Mechanistic analyses identify the glycosylphosphatidylinositol (GPI) transamidase complex and Fitm2 as representative examples of genes that become selectively required under inflammatory stress by maintaining membrane protein maturation, endoplasmic reticulum homeostasis, and resistance to oxidative stress. These findings broaden our understanding of how inflammatory cytokines influence tumor cell biology beyond transcriptional regulation and immune recognition. More broadly, the study highlights the value of incorporating physiologically relevant conditions into functional genetic screens, suggesting that conventional dependency maps capture only part of the genetic requirements for tumor survival. Applying similar approaches to other microenvironmental stresses-including hypoxia, metabolic competition, extracellular matrix remodeling, and stromal signaling-may uncover additional therapeutic opportunities for cancer immunotherapy.},
}

Humans
*Neoplasms/genetics/pathology/metabolism/immunology
*Inflammation/genetics
Tumor Microenvironment/genetics
*CRISPR-Cas Systems
Animals
Cytokines/metabolism
*Clustered Regularly Interspaced Short Palindromic Repeats
Oxidative Stress
Signal Transduction
Stress, Physiological

@article {pmid42612243,
year = {2026},
author = {Xu, S and Neupane, S and Wang, L},
title = {CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean Daphnia.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-7},
doi = {10.1139/gen-2026-0049},
pmid = {42612243},
issn = {1480-3321},
mesh = {Animals ; *Mosaicism ; *CRISPR-Cas Systems ; *Daphnia/genetics/classification ; Female ; *Gene Editing ; *Daphnia magna/genetics ; Daphnia pulex/genetics ; Genotype ; },
abstract = {Genetic mosaicism can arise from in vivo CRISPR-Cas9 gene editing, especially in the embryos. This study evaluates the extent of genetic mosaicism resulted from CRISPR-Cas9-mediated knockout for 11 genes in the freshwater microcrustacean Daphnia magna, Daphnia pulex, and Daphnia sinensis. Based on extensive genotyping data of the asexually produced progenies of successfully edited females, we find strong evidence of mosaicism in 9 of these genes. The genotyping data also suggest that the gene editing activity can take place as early as the one-cell embryo stage and extends into the 32-cell and later stages. This study establishes genetic mosaicism as an important feature of Cas9-mediated gene editing in Daphnia.},
}

Animals
*Mosaicism
*CRISPR-Cas Systems
*Daphnia/genetics/classification
Female
*Gene Editing
*Daphnia magna/genetics
Daphnia pulex/genetics
Genotype

@article {pmid42626870,
year = {2026},
author = {Ding, G and Li, Y and Xiao, Y and Li, Y and Yang, J and Zhao, R and Tang, Y and Li, B},
title = {A lock-and-key aptamer probe gates CRISPR/Cas12a trans-cleavage for antibiotic detection.},
journal = {Chemical communications (Cambridge, England)},
volume = {62},
number = {72},
pages = {17979-17982},
doi = {10.1039/d6cc04487e},
pmid = {42626870},
issn = {1364-548X},
mesh = {*Aptamers, Nucleotide/chemistry/metabolism ; *Anti-Bacterial Agents/analysis ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/metabolism ; *Biosensing Techniques/methods ; *Endodeoxyribonucleases/metabolism ; Bacterial Proteins ; },
abstract = {A lock-and-key aptamer-CRISPR/Cas12a strategy was developed to convert antibiotic recognition into signal-off fluorescence. Antibiotic binding disrupted the locking domain-maintained stem-loop structure, suppressed T4 DNA polymerase-mediated activator generation and inhibited Cas12a trans-cleavage, enabling selective antibiotic detection and providing a programmable strategy for small-molecule sensing.},
}

*Aptamers, Nucleotide/chemistry/metabolism
*Anti-Bacterial Agents/analysis
*CRISPR-Cas Systems
*CRISPR-Associated Proteins/metabolism
*Biosensing Techniques/methods
*Endodeoxyribonucleases/metabolism
Bacterial Proteins

@article {pmid42707868,
year = {2026},
author = {Lin, L and Luo, F and Liu, S and Tong, X and Xu, X and Yi, W and Deng, X and Luo, H},
title = {CRISPR-based point-of-care diagnostics for viral hepatitis: from molecular design to clinical implementation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1892898},
pmid = {42707868},
issn = {2296-4185},
abstract = {Timely etiological diagnosis of viral hepatitis is essential for surveillance, treatment initiation, linkage to care, and elimination efforts. In resource-limited settings, however, diagnostic pathways are frequently disrupted by centralized nucleic acid testing, specimen-transport requirements, delayed reporting, and loss to follow-up. CRISPR-Cas-based point-of-care testing may help shorten these pathways, but its clinical value cannot be judged by analytical sensitivity alone. This review evaluates CRISPR-Cas strategies for detecting hepatitis A, B, C, D, and E viruses by linking molecular design to virus-specific clinical and public-health decisions. We compare target selection, Cas effectors, amplification strategies, readout formats, specimen processing, genotype coverage, clinical validation, and implementation feasibility. For each virus, the evidence is evaluated in relation to the principal diagnostic need, the potential contribution of CRISPR-Cas, the maturity of the available evidence, and the remaining requirements for deployment. Current evidence is most advanced for HBV and HCV, whereas HAV, HDV, and HEV applications remain less developed or more context dependent. Future platforms should prioritize clinically meaningful detection thresholds, closed-tube sample-to-answer workflows, internal controls, genotype-diverse validation, reagent stability, non-expert usability, and transparent pathway-level cost evaluation.},
}

@article {pmid42708411,
year = {2026},
author = {Feussner, M and Birkholz, N and Lee, SY and Beisel, CL and Park, HH and Brown, CM and Fineran, PC and Weinberg, Z},
title = {An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms.},
journal = {Nucleic acids research},
volume = {54},
number = {17},
pages = {},
pmid = {42708411},
issn = {1362-4962},
support = {01IM19001//German Academic Exchange Service (DAAD)/ ; 468749960//German Research Foundation/ ; //Health Sciences Career Development Postdoctoral Fellowship/ ; //University of Otago/ ; //Bioprotection Aotearoa/ ; //Centre of Research Excellence/ ; //Tertiary Education Commission, NZ/ ; //James Cook Research Fellowship/ ; //Royal Society of New Zealand, Te Apārangi/ ; //Leipzig University/ ; },
mesh = {5' Untranslated Regions ; Operon ; *Viral Proteins/metabolism/genetics ; *Bacteriophages/genetics ; *Repressor Proteins/metabolism/genetics ; *CRISPR-Cas Systems ; Helix-Turn-Helix Motifs ; RNA, Messenger/metabolism ; Nucleotide Motifs ; Gene Expression Regulation, Bacterial ; },
abstract = {Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit bacterial CRISPR-Cas immune systems. Rapid acr gene expression upon phage entry enables CRISPR-Cas neutralization but can impact phage fitness if unregulated. Therefore, Acr production is often controlled by distinct families of co-encoded anti-CRISPR-associated (Aca) proteins, which are usually helix-turn-helix (HTH) regulators that bind DNA within acr-aca operon promoters. Previously, we demonstrated that the Aca2 family additionally represses Acr production translationally by binding structured RNA motifs within the 5' untranslated region (UTR) of the acr-aca mRNA. Here, through systematic bioinformatic analyses, we provide evidence of structured RNA motifs in the 5' UTRs of operons encoding members of other Aca families and show that Aca1 also specifically binds its cognate RNA motif. Additionally, many Aca proteins are predicted to regulate not only their own but also adjacent operons with potential anti-defence genes. Indeed, we show that Aca14, newly identified in this study, represses two predicted anti-defence operons. Aca14 is a ribbon-helix-helix domain protein, revealing regulatory diversity beyond the canonical HTH Aca family members. Collectively, our findings expand our understanding of acr regulation in mobile genetic elements and reveal novel mechanisms by which phages fine-tune anti-defence gene expression.},
}

5' Untranslated Regions
Operon
*Viral Proteins/metabolism/genetics
*Bacteriophages/genetics
*Repressor Proteins/metabolism/genetics
*CRISPR-Cas Systems
Helix-Turn-Helix Motifs
RNA, Messenger/metabolism
Nucleotide Motifs
Gene Expression Regulation, Bacterial

@article {pmid42709801,
year = {2026},
author = {Kumar, A and Nahar, N and Chouhan, D and McLean, JS and Bor, B and Dong, PT and He, X},
title = {A host-encoded prophage targets a Candidate Phyla Radiation bacterium and shapes episymbiotic interactions.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {37},
pages = {e2615890123},
doi = {10.1073/pnas.2615890123},
pmid = {42709801},
issn = {1091-6490},
support = {R01DE023810//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR)/ ; R01DE031274//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR)/ ; T90DE026110//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR)/ ; },
mesh = {*Prophages/genetics/physiology ; *Symbiosis ; Lysogeny ; Humans ; Bacteriophages ; },
abstract = {The Patescibacteriota, also known as the Candidate Phyla Radiation (CPR), represent a large lineage of ultrasmall bacteria with highly reduced genomes and obligate dependence on bacterial hosts. Although genomic analyses have revealed CRISPR-Cas and restriction-modification systems in many CPR genomes, no cognate bacteriophages (phages) have been isolated, leaving CPR-phage interactions unexplored. Nanosynbacter lyticus TM7x, the first cultivated CPR bacterium, grows episymbiotically on its host, Schaalia odontolytica XH001, in the human oral microbiome. Here, we identify Xhp1, an inducible prophage of XH001 that is preferentially activated during episymbiosis with TM7x. Released Xhp1 particles infect prophage-free XH001 via distinct strategies determined by host growth mode, establishing lysogeny under planktonic conditions but driving lytic infection during surface-associated growth. Xhp1 also binds efficiently to TM7x and exhibits limited infection under the conditions tested, indicating direct phage-CPR interactions. Importantly, TM7x modulates Xhp1 availability in a spatially dependent manner. In planktonic culture, free-floating TM7x reduces lysogenic conversion of XH001ΔXhp1, consistent with TM7x acting as a phage sink that lowers effective phage concentration. In contrast, during surface-associated growth, TM7x increases XH001ΔXhp1 susceptibility to lytic infection, likely by locally concentrating phage particles within a constrained niche. These results demonstrate that CPR bacteria can regulate viral encounter rates through spatial organization. In spatially structured environments such as oral biofilms, such modulation may shape infection dynamics and community structure. Together, this work characterizes the first CPR-targeting phage and reveals a an important role for phages in CPR-host bacteria interactions.},
}

*Prophages/genetics/physiology
*Symbiosis
Lysogeny
Humans
Bacteriophages

@article {pmid42709802,
year = {2026},
author = {Yang, X and Ouyang, H and Xu, H and Peng, L and Cui, J and Zhang, B and Huang, B and Wang, C and Li, G and Cao, X},
title = {In vivo genome-wide CRISPR screens identify FOXR1 as a suppressor of CD8[+] T cell antitumor immunity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {37},
pages = {e2534362123},
doi = {10.1073/pnas.2534362123},
pmid = {42709802},
issn = {1091-6490},
support = {82388201//National Natural Science Foundation of China/ ; 32525028//National Natural Science Foundation of China/ ; 2025-I2M-XHZY-019//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-005//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; SZS2023005//Suzhou1114 Key Laboratory Program/ ; BK20250003//Basic Research Program of Jiangsu/ ; },
mesh = {Animals ; *Forkhead Transcription Factors/genetics/metabolism/immunology ; Humans ; *CD8-Positive T-Lymphocytes/immunology ; Mice ; Lymphocyte Activation/immunology ; CRISPR-Cas Systems ; *Neoplasms/immunology/therapy/genetics ; Cell Line, Tumor ; },
abstract = {T cell dysfunction critically limits the efficacy of T cell-based immunotherapies in solid tumors, yet the intrinsic regulators of T cell dysfunction remain incompletely understood. Through an in vivo genome-wide CRISPR screen in tumor-infiltrating CD8[+] T cells, we identified Forkhead Box R1 (FOXR1) as a potent transcriptional suppressor of CD8[+] T cell effector functions. Genetic ablation of FOXR1 significantly enhanced cytokine production and cytotoxic capacity in both murine and human CD8[+] T cells, whereas its overexpression impaired T cell activation and effector molecule expression. Mechanistically, multiomics integration of RNA-seq, CUT&Tag-seq, and ATAC-seq revealed that FOXR1 binds directly to promoter regions of key effector genes, including IL2, GZMB, and PRF1, and represses their expression. Importantly, FOXR1 deletion in human anti-CD19 CAR T cells improved their efficacy against solid tumors, demonstrating that FOXR1 is a checkpoint of T cell effector function and targeting FOXR1 is a promising strategy to enhance CAR T cell efficacy against solid tumors.},
}

Animals
*Forkhead Transcription Factors/genetics/metabolism/immunology
Humans
*CD8-Positive T-Lymphocytes/immunology
Mice
Lymphocyte Activation/immunology
CRISPR-Cas Systems
*Neoplasms/immunology/therapy/genetics
Cell Line, Tumor

@article {pmid42710586,
year = {2026},
author = {Suzuki, S and Aung, MS and Matsubara, K and Kimura, Y and Ito, M and Urushibara, N and Kawaguchiya, M and Ohashi, N and Higuchi, T and Takahashi, S and Kobayashi, N},
title = {Clonal diversity and genetic characteristics of extraintestinal pathogenic Escherichia coli in northern Japan: identification of the potentially prevalent clones phylogroup B2-ST357 and ST1193.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.09.001},
pmid = {42710586},
issn = {2213-7173},
abstract = {OBJECTIVES: Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of bloodstream and urinary tract infections, often showing multiple drug resistance associated with production of extended-spectrum beta-lactamases (ESBLs). The present study aimed at revealing the clonal structure and diversity of ExPEC in northern Japan and its relation to antimicrobial resistance (AMR) profiles and determinants, and genetic features.

METHODS: Phylogenetic group and sequence type (ST) based on MLST scheme were determined for clinical isolates of ExPEC. PCR and sequencing were used to identify AMR determinants, virulence factors and CRISPR-Cas systems, along with antimicrobial susceptibility test by the broth microdilution method.

RESULTS: A total of 454 ExPEC isolates (150 from blood and 304 from urine/other specimens) were collected for 6 months. The major phylogenetic group was B2 (79.5%), and the remaining were D (9.9%), B1 (5.7%), F (3.1%), and other groups (A, C, G; 1.8% in all). Among the 68 STs identified, ST131 was the most common (33.7%), followed by ST95 (15.6%), ST357 (9.9%), ST1193 (7%), and ST73 (4%), all of which belonged to phylogroup B2. Five types of ESBL genes including the dominant blaCTX-M-15 or blaCTX-M-27 were detected in 17% of isolates, which belonged mostly to the ST131 complex. CRISPR-Cas type I-E was present mostly in phylogroup B1 and D, while I-F in 3 STs of phylogroup B2.

CONCLUSION: The potentially increased prevalence of ST357, ST1193, and animal-related clones was revealed to be novel clonal features of ExPEC in northern Japan.},
}

@article {pmid42712777,
year = {2026},
author = {Pattapulavar, V and Ramanujam, S and Yellampalli, A and Badiginchala, HS and Christopher, JG},
title = {Molecular biology and integrated strategies for activating cryptic biosynthetic gene clusters toward next-generation antibiotic discovery.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1893206},
pmid = {42712777},
issn = {2673-7647},
abstract = {Antimicrobial resistance (AMR) has been identified as one of the 21st century's severest global public health crises. AMR led to an estimated 4.95 million deaths in 2019 and will claim 10 million lives a year by 2050 in the absence of targeted interventions. During the same period, the number of novel antibiotics discovered has decreased drastically as many researchers are rediscovering known antibiotics, non-model microorganisms are poorly understood or difficult to culture and antibiotic research and development investment has declined drastically. However, high-throughput whole genome sequencing and the subsequent application of bioinformatics in bacterial and fungal genomes have shown that a numerous of cryptic or silent biosynthetic gene clusters (BGCs) remain latent at ambient laboratory conditions since their genes are transcriptionally inactive. Cryptic BGCs represent a vast source of unique secondary metabolites, many of which may yield novel antibacterial, antifungal, anti-cancer and other potentially valuable natural products. This review discusses the biological relevance of cryptic BGCs, the major limiting factors that restricts their activation and novel strategies that have been employed to activate them and exploit their potential to produce novel natural products. The review focuses on biological approaches including CRISPR-Cas mediation for the activation of cryptic BGCs, promoter engineering, pathway refactoring, and heterologous expression; biochemical strategies such as Osman, OsMAC, Precursor Feeding, Chemical Elicitation, Epigenetic Regulation and Co-cultivation and technology-based strategies such as Genome mining, Microfluidic Cultivation systems, High-Throughput Screening, Metabolomics, Molecular Networking and Artificial Intelligence and Machine Learning based prediction of BGCs and their metabolites. The use of multi-omics technologies combined with synthetic biology to achieve better discovery, characterization and large-scale production of novel natural products is also discussed herein. Finally, we will talk about the ecological significance and evolutionary advantage of cryptic BGCs' role in interactions between microorganisms, such as competition, communication, symbiosis and environmental adaptability, so as to provide a useful background for accelerating next-generation antibiotics.},
}

@article {pmid42713177,
year = {2026},
author = {Nwagwu, CS and Nwachukwu, OL and Emencheta, SC and Onugwu, AL and Ezeibe, EN and Ugwu, CN and Nnamani, PO and Tarirai, C and Ofokansi, K and Attama, A},
title = {Role of nanoclusters in the design and development of novel strategies for diagnosis and treatment of infectious diseases.},
journal = {Nanoscale advances},
volume = {},
number = {},
pages = {},
pmid = {42713177},
issn = {2516-0230},
abstract = {Despite major advances in sanitation, vaccination, and antimicrobial chemotherapy, infectious diseases continue to pose a huge threat to global health. The ever-increasing occurrences of antimicrobial resistance, emerging pathogens, and persistent diagnostic delays further exacerbate this situation. Over the years, nanotechnology has generated a lot of material platforms to address these failures, and in this study, we critically examine nanoclusters-ultrasmall, atomically precise assemblies (<2 nm cores) with discrete electronic states, as an under-recognized but potentially transformative class of materials for infectious disease diagnostics and therapeutics. Their quantized optical properties, precision ligand chemistry, and unusually high surface-to-volume ratios enable behaviours fundamentally inaccessible to larger nanomaterials, including ratiometric fluorescence reporting, rapid redox-driven antimicrobial activity, and programmable bio-recognition at near-molecular resolution. First, we disentangle NCs from larger nanomaterials by focusing on the consequences of discrete electronic states, ultrasmall hydrodynamic radii, and well-defined ligand shells for transport, clearance, and interactions with pathogens and host-derived biomolecules. Furthermore, the review synthesizes advances in NC-enabled diagnostics, including DNA and aptamer templated Au, Ag, and Cu NC probes, CRISPR/Cas integrated ratiometric sensors, and nanozyme-based readouts that routinely achieve single colony-forming unit or sub-femtomolar detection of bacterial, viral, fungal, and protozoan nucleic acids and antigens. On the therapeutic side, we discuss how the same structural characteristics can be exploited to engineer NCs that mediate controlled ROS generation, membrane and biofilm disruption, quorum sensing interference, photothermal and NIR II photodynamic therapy, and ligand-directed drug delivery, with case studies spanning multidrug-resistant bacteria, opportunistic fungi, and selected parasitic infections. At the same time, we looked at some of the major barriers to clinical translation that remain unaddressed. We show with this study that nanoclusters are not merely "smaller nanoparticles" but a distinct chemical system, capable of enabling modular, multiplexed, and clinically relevant infectious disease interventions. To realize this potential, future work must couple atomic-level design with rigorous pharmacokinetic, toxicodynamic, and translational engineering frameworks.},
}

@article {pmid42713468,
year = {2026},
author = {Riaz Ahmed, S and Khan, J and Ijaz, I and Ali, Z and Rasul, I and Aslam, M and Ud-Din, N and Liu, Y and Tariq, MS and Skalicky, M and Tan, DKY},
title = {CRISPR-Cas technologies for precision genome editing in plants: advances, applications, and future perspectives.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1902159},
pmid = {42713468},
issn = {1664-462X},
abstract = {Developing climate-smart crops with enhanced crop productivity, nutritional quality, resistance to biological and environmental stressors is vital for global food security. While hybrid breeding forms the cornerstone of modern crop improvement, conventional breeding approaches are limited by genetic barriers and prolonged breeding cycles. CRISPR-Cas based genome editing has revolutionized plant biology by allowing precise, efficient, and multiplex genetic modifications. This review provides a comprehensive synthesis of a recent advances in CRISPR-Cas technologies and their strategic applications in crop genetics and hybrid breeding. We summarize major genome-editing strategies, including gene knock-out, base editing (BE), knock-in, gene replacement, epigenome editing, and transcriptional regulation. Furthermore, we contrast stable, transient, and DNA-free delivery systems, highlighting ribonucleoprotein (RNP)-mediated delivery for minimizing off-target effects and avoiding transgene integration. We showcase how these technologies accelerate hybrid breeding by engineering male sterility systems, fixing heterosis, and generating high-throughput mutant libraries for trait discovery. Finally, we synthesize major bottlenecks in tissue culture-independent transformation and delivery systems, while outlining how emerging paradigms like de novo domestication and synthetic biology will shape the future of climate-resilient agriculture.},
}

@article {pmid42714094,
year = {2026},
author = {Zheng, S and Li, X and Li, F and Ren, X and Chen, J and Zou, Y and Yang, FH and Xia, Y and Tan, W},
title = {Generation and Phenotypic Characterization of a CRISPR/Cas9-Engineered Cracd-Deficient Mouse Model for Post-Myocardial Infarction Remodeling Studies.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/71451},
pmid = {42714094},
issn = {1940-087X},
mesh = {Animals ; Mice ; *Myocardial Infarction/genetics/physiopathology/pathology ; *Disease Models, Animal ; Mice, Inbred C57BL ; *CRISPR-Cas Systems ; *Ventricular Remodeling ; Phenotype ; Male ; },
abstract = {Myocardial infarction (MI) remains a major cause of morbidity and mortality worldwide. This protocol describes a method for generating and characterizing a Cracd-deficient mouse line on the C57BL/6N background using CRISPR/Cas9 technology. Zygotes were co-injected with Cas9 mRNA, a gRNA construct, and a donor template designed to generate a 3153-bp genomic deletion. The edited allele was confirmed by PCR genotyping and Sanger sequencing. To assess the functional role of CRACD in post-MI remodeling, Cracd-deficient and wild-type (WT, C57BL/6N) mice underwent MI induced by permanent ligation of the left anterior descending coronary artery. On postoperative day 7, cardiac function and left ventricular wall motion were assessed using transthoracic echocardiography and speckle-tracking strain imaging, followed by histopathological evaluation with H&E and Masson's trichrome staining. Representative results showed that Cracd-deficient mice exhibited reduced ventricular dilation and preserved systolic function compared to WT controls. This protocol provides a reliable experimental platform for mechanistic studies of CRACD in cardiac pathophysiology.},
}

Animals
Mice
*Myocardial Infarction/genetics/physiopathology/pathology
*Disease Models, Animal
Mice, Inbred C57BL
*CRISPR-Cas Systems
*Ventricular Remodeling
Phenotype
Male

@article {pmid42714611,
year = {2026},
author = {Yaoyu, T and Xiang, X and Peizhi, Y and Xiaoxia, S},
title = {Genetic transformation of forage crops: comparative barriers, evidence, and emerging strategies.},
journal = {Plant cell reports},
volume = {45},
number = {10},
pages = {},
pmid = {42714611},
issn = {1432-203X},
support = {32302478//National Natural Science Foundation of China/ ; 2452024004//Northwest A&F University/ ; },
mesh = {*Crops, Agricultural/genetics ; *Transformation, Genetic ; Plants, Genetically Modified/genetics ; *Fabaceae/genetics ; *Poaceae/genetics ; Gene Transfer Techniques ; CRISPR-Cas Systems/genetics ; },
abstract = {Forage crops include phylogenetically and biologically distinct legumes and grasses, and their genetic transformation is constrained by different combinations of host response, DNA-delivery efficiency, regeneration competence, genotype dependence, and genome stability. This review critically compares evidence from forage legumes and forage grasses rather than treating these groups as a single transformation category. We evaluate Agrobacterium-mediated transformation, protoplast-based delivery, particle bombardment, CRISPR/Cas-enabled applications, developmental regulators (DRs), viral vectors, and nanomaterial-mediated delivery according to four practical outcomes: reproducibility across genotypes, recovery of regenerated plants, heritable transmission, and genetic stability. Direct evidence in forage crops shows that protocol performance is strongly species-, genotype-, explant-, and endpoint-dependent; efficiencies based on transient reporters or resistant callus therefore cannot be directly equated with stable, fertile events. DR-assisted regeneration has direct proof of concept in recalcitrant forage grasses, whereas stable nanomaterial-mediated transformation and virus-induced heritable editing remain unvalidated in forage crops. We conclude that current progress is best interpreted as the engineering of interacting delivery and regeneration constraints, not as a universal transition to genotype-independent transformation. Priority should be given to standardized outcome reporting, multi-genotype and inter-laboratory validation, controlled DR expression, and rigorous molecular and phenotypic assessment of regenerated plants.},
}

*Crops, Agricultural/genetics
*Transformation, Genetic
Plants, Genetically Modified/genetics
*Fabaceae/genetics
*Poaceae/genetics
Gene Transfer Techniques
CRISPR-Cas Systems/genetics

@article {pmid42715083,
year = {2026},
author = {Jiang, Q and Xu, R and Lin, Z and Sun, C and Ye, F and Ye, Y and Lin, D and Li, Z and Mai, J and Lin, Z and Qu, J and Deng, X and Ge, C and Wang, D},
title = {Harmonizing amplification and cleavage kinetics through crRNA scaffold mutation enables robust one-pot CRISPR-Cas12 diagnostics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {37},
pages = {e2613134123},
doi = {10.1073/pnas.2613134123},
pmid = {42715083},
issn = {1091-6490},
support = {2024YFC2310203//the Key National R&D Program of China/ ; SYSPG20241211173949065//the Shenzhen Key Laboratory of Biochip/ ; JCYJ20240813113233044//the Shenzhen Science and Technology Program/ ; S202510570075//College Students' Innovative Entrepreneurial Training Plan Program/ ; S202510570072//College Students' Innovative Entrepreneurial Training Plan Program/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; Kinetics ; Humans ; *Nucleic Acid Amplification Techniques/methods ; *SARS-CoV-2/genetics/isolation & purification ; CRISPR-Associated Proteins/genetics/metabolism ; Rapid Diagnostic Tests ; Mutation ; Endodeoxyribonucleases/genetics/metabolism ; Bacterial Proteins ; },
abstract = {CRISPR-based diagnostics (CRISPR-Dx) integrated with isothermal nucleic acid amplification have emerged as a promising strategy for point-of-care molecular testing. Their practical deployment, however, remains constrained by workflow-related limitations. Conventional two-step formats are laborious and highly susceptible to aerosol contamination during amplicon transfer, whereas simplified one-pot formats often suffer from reduced sensitivity because amplification and CRISPR-mediated cleavage compete kinetically within the same reaction vessel. In this work, we present a broadly applicable one-pot detection strategy termed mutant scaffold-mediated RPA-CRISPR/Cas12a (MS-CRISPR). This approach introduces rationally designed point mutations into the crRNA scaffold to moderately attenuate Cas12a activation and cleavage kinetics. Such kinetic tuning prevents the enzyme from prematurely depleting nascent RPA amplicons, a common source of signal loss in wild-type systems. By delaying cleavage until sufficient amplification products have accumulated, MS-CRISPR markedly enhances endpoint signal output. Using this kinetically balanced system, we achieved a limit of detection of 1 copy/μL for both SARS-CoV-2 and influenza A virus within 15 min, while preserving a fully closed-tube workflow that minimizes aerosol contamination and simplifies operation. We coupled the assay with an instrument-free lateral-flow readout and an ultraportable, multiplex, low-cost microfluidic platform (portable wireless isothermal nucleic acid detection). Clinical validation with patient samples showed 100% sensitivity and specificity for both viral targets. Collectively, MS-CRISPR establishes a sensitive, versatile, and field-deployable platform for rapid pathogen screening.},
}

*CRISPR-Cas Systems/genetics
Kinetics
Humans
*Nucleic Acid Amplification Techniques/methods
*SARS-CoV-2/genetics/isolation & purification
CRISPR-Associated Proteins/genetics/metabolism
Rapid Diagnostic Tests
Mutation
Endodeoxyribonucleases/genetics/metabolism
Bacterial Proteins

@article {pmid42716374,
year = {2026},
author = {Lau, CH and Xia, Q and Liang, Q and Guo, R and Zhu, H},
title = {Opto-CRISPR technologies in translational neuropharmacology.},
journal = {Neuropharmacology},
volume = {301},
number = {},
pages = {111185},
doi = {10.1016/j.neuropharm.2026.111185},
pmid = {42716374},
issn = {1873-7064},
abstract = {Opto-CRISPR (optically controlled CRISPR/Cas) represents a major advancement in precision neurology by enabling localized gene editing within the nervous system at precise times and locations. While preclinical studies still rely largely on classical CRISPR/Cas systems, opto-CRISPR offers unprecedented opportunities to safely treat neurological diseases at their genetic roots. It achieves this by spatiotemporally correcting pathogenic mutations, halting toxic protein accumulation, repairing neurons, rebuilding neural circuitry, and accelerating drug discovery through highly realistic disease models. This review discusses this emerging field and its transformative potential for translational neuropharmacology, focusing on therapies for neurodevelopmental and neurodegenerative disorders. Opto-CRISPR is classified into four generations: Generation 1 (light-controlled Cas protein systems), Generation 2 (light-activated guide RNA systems), Generation 3 (light-controlled inhibitor systems), and Generation 4 (NIR upconversion and epigenetic multiplexing). Their working mechanisms, applications, advantages, and limitations are comprehensively described. We also critically discuss how opto-CRISPR offers distinct advantages over traditional biologics and remote modalities (e.g., small-molecule drugs, monoclonal antibodies, antisense oligonucleotides, viral-mediated gene therapy, magnetogenetics, and sonogenetics) in neuropharmacology. Finally, we address current challenges and the therapeutic outlook for the clinical translation of opto-CRISPR.},
}

@article {pmid42705625,
year = {2026},
author = {Sharma, S and Subramanyam, R},
title = {Carotenoids in Stress Tolerance: Current Understanding and Future Prospects.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71095},
pmid = {42705625},
issn = {1399-3054},
support = {BT/PR55080/BSA/33/289/2024//Department of Biotechnology, Ministry of Science and Technology, India/ ; 6-8/2018 (IC)//Joint UGC-ISF Research/ ; CRG/2020/000489//Science & Engineering Research Board/ ; no. 38 (1504)/21/EMR-ll//Council of Scientific and Industrial Research, India/ ; UoH/IoE/RC1/RC1-20-019//Institute of Eminence/ ; UoH/IoE/IIRC-23-004//Institute of Eminence/ ; },
mesh = {*Carotenoids/metabolism ; *Stress, Physiological ; Photosynthesis/physiology ; Signal Transduction ; Plants/metabolism ; Adaptation, Physiological ; },
abstract = {Carotenoids are ubiquitous isoprenoid metabolites whose biological significance extends far beyond their classical roles as antioxidants and light-harvesting pigments. Across the tree of life, these molecules exhibit remarkable structural and functional diversity, enabling organisms to fine-tune photoprotection, redox homeostasis, membrane organization, and stress-responsive signaling. In this review, we provide a conceptual synthesis of carotenoid diversity and function across organisms, with emphasis on how carotenoid composition and accumulation are dynamically regulated under environmental and biotic stresses. We highlight stress-induced carotenoid plasticity, manifested as selective accumulation, rerouting of pathways, and the production of signaling apocarotenoids as a central adaptive strategy across photosynthetic organisms. Finally, we discuss emerging evidence and competing hypotheses regarding the mechanistic diversity of non-photochemical quenching and the evolving yet debated role of carotenoids in energy-dependent quenching. Together, this review emphasizes carotenoids as dynamic metabolic regulators that integrate many facets of photosynthetic performance, stress responses and signaling.},
}

*Carotenoids/metabolism
*Stress, Physiological
Photosynthesis/physiology
Signal Transduction
Plants/metabolism
Adaptation, Physiological

@article {pmid42706676,
year = {2026},
author = {Camargo, JA and Lee, MC and Souza, MM and Silva, LPD and Boas, GCV and Silva, KSD and Mioshi, CM and Pimenta, RCA and Candido, P and Silva, IAD and Trarbach, EB and Leite, KRM and Nahas, WC and Reis, STD},
title = {MMP9 Knockout by CRISPR-Cas9 Reduces Bladder Cancer Malignancy But Does Not Synergize With BCG and Anti-PD-L1 in an Orthotopic Mouse Model.},
journal = {IUBMB life},
volume = {78},
number = {9},
pages = {e70130},
pmid = {42706676},
issn = {1521-6551},
support = {2022/08864-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/02288-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Mice ; *Matrix Metalloproteinase 9/genetics ; Female ; *CRISPR-Cas Systems ; *Urinary Bladder Neoplasms/pathology/genetics/therapy/drug therapy ; *B7-H1 Antigen/antagonists & inhibitors ; *BCG Vaccine/pharmacology ; Mice, Inbred C57BL ; Cell Line, Tumor ; *Immune Checkpoint Inhibitors/pharmacology ; Disease Models, Animal ; Gene Expression Regulation, Neoplastic ; Mice, Knockout ; Humans ; },
abstract = {Bladder cancer (BC) is the 10th most common cancer worldwide, accounting for approximately 5% of new cases. Several factors contribute to tumor progression, including increased MMP9. Recently, CRISPR-Cas9 and immunotherapy have offered high specificity for treatments; therefore, we edited MMP9 using CRISPR-Cas9 methodology to inhibit metastatic mechanisms and evaluated potential synergy with BCG and anti-PD-L1 therapy. We performed CRISPR-Cas9 gene editing using an RNP complex in the MB49 murine BC cell line. Gene expression of MMPs, integrins, and BAX was analyzed, along with protein expression. Cells were divided into a Scramble control group and CRISPR-Cas9 for the MMP9 edited group (MMP9-/-). Female C57BL/6 mice received orthotopic BC cells (scramble and MMP9-/- groups) treated with BCG and anti-PD-L1. Statistical analyses were performed using t test or ANOVA. MMP9 gene and protein expression were reduced in the MMP9-/- group compared with the scramble group. No differences were observed in other MMPs. Decreased ITGB3, increased BAX gene expression, as well as reduced migration and adhesion to ECM were observed in the MMP9-/- group. Animals in the scramble group showed greater weight loss and lower survival than treated groups. Overall, MMP9 modulated key cellular mechanisms, but did not show synergistic effects with BCG and anti-PD-L1 in vivo.},
}

Animals
Mice
*Matrix Metalloproteinase 9/genetics
Female
*CRISPR-Cas Systems
*Urinary Bladder Neoplasms/pathology/genetics/therapy/drug therapy
*B7-H1 Antigen/antagonists & inhibitors
*BCG Vaccine/pharmacology
Mice, Inbred C57BL
Cell Line, Tumor
*Immune Checkpoint Inhibitors/pharmacology
Disease Models, Animal
Gene Expression Regulation, Neoplastic
Mice, Knockout
Humans

@article {pmid42707485,
year = {2026},
author = {Fabrizi, A and Valenti, M and Zacchino, S and Russo, K and Baschetti, E and De Rosa, L and De Luca, M},
title = {Gene therapy for genodermatoses at the crossroads of innovation and clinical translation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1901459},
pmid = {42707485},
issn = {2296-4185},
abstract = {Inherited genodermatoses are a heterogeneous group of rare monogenic disorders. Among these, epidermolysis bullosa (EB) and ichthyoses represent paradigmatic disorders characterized by severe skin fragility and hyperkeratosis, respectively, and impaired barrier function, often with profound effects on quality of life and systemic health. Current management remains largely palliative, underscoring the urgent need for disease-modifying therapies. Over the past 2 decades, advances in epithelial stem cell biology, vector engineering and genome editing technologies have transformed the therapeutic landscape for genodermatoses. Ex vivo gene therapy has provided the first proof that genetically corrected epidermal stem cells can achieve long-term tissue regeneration in EB skin patients, establishing a new paradigm for regenerative medicine. In parallel, the emergence of programmable genome engineering platforms, including CRISPR/Cas nucleases, base editors and prime editors, have enabled increasingly precise strategies for mutation-specific correction in both recessive and dominant disorders. Furthermore, the development of in vivo topical approaches is expanding the possibility of directly targeting the skin. Despite these advances, substantial translational barriers continue to limit broad clinical implementation. Efficient and durable targeting of epidermal stem cells within a highly regenerative tissue, together with safe delivery across the skin barrier, stringent control of off-target activity, scalable manufacturing and demonstration of long-term safety, remain major challenges for the clinical translation of these approaches. In this Review, we discuss the current state of gene therapy for genodermatoses, highlighting key clinical milestones, emerging genome editing technologies and next-generation delivery systems. We further examine the biological and regulatory challenges that need to be overcome to bridge the gap between experimental innovation and clinically accessible therapies for patients with inherited skin diseases.},
}

@article {pmid42707723,
year = {2026},
author = {Tao, J and Zeng, B and Bi, C and Xu, M and Gu, X and Jing, D and Sun, J},
title = {An RCA-Coupled CRISPR/Cas12a Cascade-Enhanced SERS Platform for Ultrasensitive Detection of Exosomal miRNA-21 in Colorectal Cancer Serum.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {622664},
pmid = {42707723},
issn = {1178-2013},
mesh = {*MicroRNAs/blood/genetics ; *Spectrum Analysis, Raman/methods ; Humans ; *Colorectal Neoplasms/blood/genetics/diagnosis ; *CRISPR-Cas Systems/genetics ; *Exosomes/chemistry/genetics ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Limit of Detection ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {PURPOSE: Ultra-sensitive detection of exosomal miR-21 is crucial for the early diagnosis of colorectal cancer. This study aims to develop a cascade amplification platform based on surface-enhanced Raman scattering (SERS), combining rolling circle amplification (RCA) and CRISPR/Cas12a, to enable ultra-sensitive quantitative detection of exosomal miR-21.

METHODS: A SERS substrate was constructed using streptavidin-modified concave gold nanocubes (CGNs), and gold double-stranded probes loaded with Raman reporter molecules were used as SERS probes. The two components are controllably linked via a single-stranded DNA molecule with a thiol group at one end and biotin at the other, forming a stable detection system. Target-triggered RCA generates a repeat sequence, which, under the mediation of crRNA, activates Cas12a cleavage, causing the probe to be released from the substrate surface and resulting in a significant attenuation of the SERS signal.

RESULTS: This platform achieves three-stage cascading signal amplification via RCA, CRISPR/Cas12a, and SERS, with a detection limit at the femto-mole (fM) level and a total detection time of approximately 80 minutes. The results were consistent with those of qRT-PCR, demonstrating high sensitivity, high specificity, and reliability.

CONCLUSION: This study proposes an RCA-CRISPR-SERS cascade amplification platform that provides a highly sensitive and specific method for detecting miR-21 in exosomes, offering potential clinical value for the early diagnosis and dynamic monitoring of colorectal cancer.},
}

*MicroRNAs/blood/genetics
*Spectrum Analysis, Raman/methods
Humans
*Colorectal Neoplasms/blood/genetics/diagnosis
*CRISPR-Cas Systems/genetics
*Exosomes/chemistry/genetics
Gold/chemistry
Metal Nanoparticles/chemistry
Limit of Detection
Nucleic Acid Amplification Techniques/methods

@article {pmid42628215,
year = {2026},
author = {Eom, KH and Gim, GM and Lee, MG and Choi, BY and Kim, DY and Jung, D and Heo, S and Yum, SY and Jang, G},
title = {Evaluation of germline transmission of electroporation-mediated double gene-edited cattle lines.},
journal = {Theriogenology},
volume = {266},
number = {},
pages = {118142},
doi = {10.1016/j.theriogenology.2026.118142},
pmid = {42628215},
issn = {1879-3231},
mesh = {Animals ; Cattle/genetics ; Male ; *Electroporation/veterinary ; Female ; *Gene Editing/veterinary/methods ; CRISPR-Cas Systems ; Gene Knockout Techniques/veterinary ; Germ Cells ; Myostatin/genetics ; Animals, Genetically Modified ; Spermatozoa ; Galactosyltransferases/genetics ; },
abstract = {Gene editing in livestock using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) offers a promising approach for genetic improvement in cattle. This study evaluated germline transmission and mutation stability of double-knockout cattle generated by zygote electroporation. Previously reported myostatin/beta-lactoglobulin (MSTN/BLG) and newly generated α-1,3-galactosyltransferase (GGTA1/BLG) double-knockout cattle were produced using CRISPR/Cas9-mediated genome editing. Targeted deep sequencing demonstrated extensive somatic mosaicism across multiple tissues. Computer-assisted sperm analysis (CASA) demonstrated normal sperm motility in MSTN/BLG double-knockout males. Fertilization of wild-type oocytes produced heterozygous embryos, with mutation frequencies of 37.76 ± 10.74% at the MSTN locus and 54.80 ± 7.73% at the BLG locus, as assessed by T7 endonuclease I (T7E1) assay. MSTN/BLG double-knockout sperm were subsequently used for embryo production and for artificial insemination of GGTA1/BLG double-knockout females. Healthy offspring were successfully obtained (n = 3), alongside one stillborn calf. Targeted deep sequencing of all four progenies revealed highly variable allele frequencies that deviated substantially from the approximately 50% expected for heterozygous germline transmission. In contrast, whole-genome sequencing (WGS) results were consistent with Mendelian expectations, underscoring the limitations of PCR-based targeted sequencing for assessing germline transmission in mosaic founders. These results show that CRISPR/Cas9-edited embryos generated by electroporation can develop into healthy, sexually mature cattle capable of germline transmission. While variable transmission rates were observed owing to founder mosaicism, non-mosaic F1 offspring were successfully generated. However, direct, embryo-mediated gene-editing strategies remain technically and economically challenging for large-scale commercial calf production, and reports in cattle are limited. This study provides a reference for future applications of gene-edited embryos and their germline propagation.},
}

Animals
Cattle/genetics
Male
*Electroporation/veterinary
Female
*Gene Editing/veterinary/methods
CRISPR-Cas Systems
Gene Knockout Techniques/veterinary
Germ Cells
Myostatin/genetics
Animals, Genetically Modified
Spermatozoa
Galactosyltransferases/genetics

@article {pmid42704380,
year = {2026},
author = {Paenkaew, S and Sinthao, O and Thapthim, T and Mahakkaprateep, S and Cheukaw, A and Keawmanee, S and Euppayo, T and Tungtrakanpoung, R and Teapunvong, W and Nganvongpanit, K and Buddhachat, K},
title = {A cost-effective and rapid TE-based DNA extraction for near point-of-care detection of Babesia spp. by RPA/CRISPR-Cas12a.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42704380},
issn = {1573-4978},
support = {R2568E050//Research Grant Agreement for Program Director, Faculty of Science, Naresuan University/ ; N42A650332//the National Research Council of Thailand (NRCT)/ ; R2565A060//the Faculty of Science, Naresuan University, Thailand/ ; R2566C051//the Global and Frontier Research University Fund, Naresuan University, Thailand/ ; },
mesh = {*Babesia/genetics/isolation & purification ; Animals ; *Babesiosis/diagnosis/genetics/parasitology ; *Nucleic Acid Amplification Techniques/methods/economics ; *DNA, Protozoan/genetics/isolation & purification ; CRISPR-Cas Systems/genetics ; Cost-Benefit Analysis ; Rapid Diagnostic Tests ; Point-of-Care Systems ; Dogs ; Humans ; },
abstract = {BACKGROUND: Babesia spp. infects a wide range of mammals, including domestic animals, wildlife, and humans, highlighting the need for rapid diagnostics. This study developed a near point-of-care method combining rapid DNA extraction, recombinase polymerase amplification (RPA), and CRISPR-Cas12a for Babesia detection.

METHODS AND RESULTS: The workflow includes three steps: DNA extraction, RPA amplification, and CRISPR-Cas12a signal detection. Five blood DNA extraction methods were evaluated: DNeasy kit, boiling, Tris-EDTA (TE) buffer, methanol-based, and Chelex®100. The commercial kit, boiling method, and TE buffer extraction yielded positive results using RPA/CRISPR-Cas12a based on the cytochrome c oxidase subunit I (COI) gene. The TE buffer extraction and boiling methods were further optimized by RPA/CRISPR-Cas12a assay using Babesia-specific primers based on the 18S rRNA gene. All these extraction methods produced results comparable to the commercial kit. The TE buffer extraction was selected due to its simplicity and speed. The RPA/CRISPR-Cas12a assay specifically detected Babesia spp., including B. vogeli, B. gibsoni, and B. ovata. The limit of detection using TE-extracted DNA was 104 copies per reaction, lower than that achieved with the commercial kit (103 copies per reaction). Evaluation of rapid DNA extraction for Babesia spp. detection by the RPA/CRISPR-Cas12a assay using seven bovine and eight canine blood samples showed complete concordance between the TE buffer extraction and the commercial kit, with six positive samples detected.

CONCLUSIONS: The TE buffer extraction offered a low-cost, simple, and equipment-minimal approach suitable for combination with RPA/CRISPR-Cas12a diagnostics, enabling rapid detection of Babesia spp. in resource-limited or field settings.},
}

*Babesia/genetics/isolation & purification
Animals
*Babesiosis/diagnosis/genetics/parasitology
*Nucleic Acid Amplification Techniques/methods/economics
*DNA, Protozoan/genetics/isolation & purification
CRISPR-Cas Systems/genetics
Cost-Benefit Analysis
Rapid Diagnostic Tests
Point-of-Care Systems
Dogs
Humans

@article {pmid42704632,
year = {2026},
author = {Guo, Y and Tan, X},
title = {Specificity and Regulatory Mechanism of Metal Ions in Cas12a Enzymatic Cleavage Activity.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/mtomcs/mfag027},
pmid = {42704632},
issn = {1756-591X},
abstract = {Metal ions play key roles in both physiological and pathological processes. The activity of nearly all nucleases depends on metal ions as cofactors. CRISPR-Cas system is widely used in gene editing and nucleic acid detection, and its ongoing development and frontier research have attracted significant attention. This study aims to explore and elucidate the effects of various metal ions on Cas12a-catalysed cleavage reactions including their specificity and regulatory mechanisms. Here, we found that certain metal ions significantly affected both the cleavage activity and the reaction specificity of Cas12a. Metal ions mediate enzyme-substrate binding by increasing the affinity between Cas12a and single-stranded DNA (ssDNA). In particular, unlike other metal ions, Mn2+ can achieve cleavage of ssDNA by only activating the catalytic domain without requiring the entire Cas12a. Structural alignment and site-directed mutagenesis of the active site revealed the structural basis of Cas12a catalysis and elucidated how metal ions influence its catalytic reaction in terms of specificity and regulatory mechanism. These results provide a theoretical foundation and offer innovative perspectives for the application of Cas12a-based enzyme technology.},
}

@article {pmid42283406,
year = {2026},
author = {Zhu, Y and Cao, D and Guo, T and Zhang, X and Luo, Y and Li, X and Yang, H and Zhang, M and Guo, S and Song, F},
title = {RNase III-deficient Bacillus thuringiensis enables stable dsRNA production and enhances HD1 activity against Spodoptera frugiperda.},
journal = {Pest management science},
volume = {82},
number = {10},
pages = {9889-9898},
doi = {10.1002/ps.71023},
pmid = {42283406},
issn = {1526-4998},
support = {CAAS-CSCB-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 024YFD1200203//National Key R&D Program of China/ ; 32372623//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Spodoptera/growth & development/genetics ; *Bacillus thuringiensis/genetics/enzymology ; *RNA, Double-Stranded/metabolism/genetics ; *Ribonuclease III/genetics/metabolism/deficiency ; *Pest Control, Biological/methods ; RNA Interference ; Larva/growth & development/genetics ; *Bacterial Proteins/genetics/metabolism ; CRISPR-Cas Systems ; },
abstract = {BACKGROUND: Spodoptera frugiperda is one of the most important invasive agricultural pests in China. Integrating RNA interference (RNAi) with Bacillus thuringiensis (Bt)-based biocontrol represents a promising strategy for pest control. However, efficient dsRNA production in Bt remains challenging as endogenous RNase activity limits dsRNA stability and accumulation.

RESULTS: In this study, an RNase III-deficient Bt strain, DBΔrnc, was generated using an optimized CRISPR-Cas9 system. Deficiency of RNase III markedly enhanced intracellular dsRNA accumulation. A hairpin dsRNA construct exhibited higher transcript levels than the dual-promoter construct, especially in the DBΔrnc background. Oral delivery of Bt expressed hairpin dsRNA targeting the endochitinase gene SfCHI of S. frugiperda induced effective gene silencing and caused pupation defects. Moreover, co-application with Bt HD1 strain significantly increased larval mortality in both neonate and 2[nd]-instar larvae.

CONCLUSION: Collectively, our findings highlight that the RNase III-deficient strain DBΔrnc is an efficient chassis for dsRNA expression. Furthermore, the enhanced insecticidal activity from co-application of DBΔrnc(hpdsCHI) and HD1 demonstrates the feasibility of integrating RNAi with Bt-based pest control. © 2026 Society of Chemical Industry.},
}

Animals
*Spodoptera/growth & development/genetics
*Bacillus thuringiensis/genetics/enzymology
*RNA, Double-Stranded/metabolism/genetics
*Ribonuclease III/genetics/metabolism/deficiency
*Pest Control, Biological/methods
RNA Interference
Larva/growth & development/genetics
*Bacterial Proteins/genetics/metabolism
CRISPR-Cas Systems

@article {pmid42537346,
year = {2026},
author = {Yang, G and Qin, H and Wang, Q and Cheng, J and Du, L and Fan, A and Lin, W and Huang, J and Hu, X and Li, Y and Wang, H},
title = {In vivo CRISPR screening identifies LTA4H as a target for potentiating immunotherapy efficacy via the LTB4-neutrophil axis.},
journal = {International immunopharmacology},
volume = {187},
number = {},
pages = {117213},
doi = {10.1016/j.intimp.2026.117213},
pmid = {42537346},
issn = {1878-1705},
mesh = {Animals ; *Epoxide Hydrolases/genetics/metabolism ; *Neutrophils/immunology ; *Leukotriene B4/metabolism ; Mice ; Humans ; Signal Transduction ; *Immunotherapy/methods ; Receptors, Leukotriene B4/antagonists & inhibitors/metabolism ; Mice, Inbred C57BL ; Cell Line, Tumor ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; CRISPR-Cas Systems ; CD8-Positive T-Lymphocytes/immunology ; Killer Cells, Natural/immunology ; },
abstract = {Despite the clinical success of PD-1 blockade, therapeutic resistance remains a major barrier. Using an in vivo CRISPR-Cas9 screen with a metabolism-focused sgRNA library in MC38 and B16 syngeneic tumor models, we identified leukotriene A4 hydrolase (LTA4H) as a candidate regulator of PD-1 resistance. Lta4h ablation was associated with enhanced PD-1 responsiveness, increased CD8+ T and NK-cell infiltration and function, and reduced myeloid accumulation. Single-cell and spatial transcriptomic analyses showed that LTA4H is expressed in both malignant and myeloid compartments, with LTA4H-high tumor regions associated with myeloid-enriched niches and TGF-β related signaling. Mechanistically, hypoxia-induced HIF1α upregulated Lta4h in tumor cells, supporting tumor cells as one relevant source of LTA4H/LTB4. LTA4H-LTB4 signaling was linked to myeloid remodeling and TGF-β1 production in LTB4-conditioned neutrophils. Pharmacological blockade of LTB4 receptor signaling with the BLT1 antagonist CP-105696 improved tumor control in combination with PD-1 blockade. These findings identify intratumoral LTA4H-LTB4 signaling as a metabolic-immune pathway associated with suppressive myeloid remodeling and support further investigation of LTB4 receptor blockade to improve PD-1 blockade responses.},
}

Animals
*Epoxide Hydrolases/genetics/metabolism
*Neutrophils/immunology
*Leukotriene B4/metabolism
Mice
Humans
Signal Transduction
*Immunotherapy/methods
Receptors, Leukotriene B4/antagonists & inhibitors/metabolism
Mice, Inbred C57BL
Cell Line, Tumor
Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism
CRISPR-Cas Systems
CD8-Positive T-Lymphocytes/immunology
Killer Cells, Natural/immunology

@article {pmid42659797,
year = {2026},
author = {Fu, R and Hong, J and Qu, Q and Hong, Z and Jiang, Q and Xianyu, Y},
title = {CRISPR-Cas12a-based querying of DNA-stored MRI and PET imaging data.},
journal = {Medical image analysis},
volume = {114},
number = {},
pages = {104272},
doi = {10.1016/j.media.2026.104272},
pmid = {42659797},
issn = {1361-8423},
mesh = {*Positron-Emission Tomography/methods ; *Magnetic Resonance Imaging/methods ; *DNA/genetics ; Sensitivity and Specificity ; Reproducibility of Results ; *Information Storage and Retrieval/methods ; *CRISPR-Cas Systems/genetics ; Humans ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; },
abstract = {Storing magnetic resonance imaging (MRI) and positron emission tomography (PET) imaging data in DNA offers a promising solution for the long-term archival management of rapidly expanding biomedical image volumes. However, querying these data typically requires polymerase chain reaction and sequencing, which increases readout complexity and retrieval latency. Here, we propose a CRISPR-Cas12a-based querying strategy that leverages the programmability of CRISPR RNA (crRNA) for precise matching with identifier (ID) sequences. In this approach, crRNA functions as a query tool that identifies matching IDs and triggers detectable signals. Through a one-to-one mapping between ID and payload sequences established during encoding, the corresponding image data can be retrieved upon query. Computational simulations demonstrate over 99% query accuracy for both MRI and PET data using crRNA. CRISPR-Cas12a cleavage assays and molecular docking further validate the high specificity of crRNA-ID recognition. This work demonstrates the potential of CRISPR-Cas12a for biochemical querying of DNA-encoded biomedical imaging data, enabling targeted access to indexed sequences.},
}

*Positron-Emission Tomography/methods
*Magnetic Resonance Imaging/methods
*DNA/genetics
Sensitivity and Specificity
Reproducibility of Results
*Information Storage and Retrieval/methods
*CRISPR-Cas Systems/genetics
Humans
Bacterial Proteins
Endodeoxyribonucleases
CRISPR-Associated Proteins

@article {pmid42700392,
year = {2026},
author = {Pittman, CC and Xu, C and Catchpole, RJ and Garrett, S and Fuchs, R and Chu, X and Makarova, KS and Koonin, EV and Zhao, P and Wells, L and Graveley, BR and Ke, A and Terns, MP},
title = {Type IV-C CRISPR-Cas effector complexes recognize double-stranded DNA and switch on collateral cleavage of ssDNA and RNA.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117939},
doi = {10.1016/j.celrep.2026.117939},
pmid = {42700392},
issn = {2211-1247},
abstract = {Type IV-C CRISPR-Cas systems remain enigmatic compared to other class 1 systems. Here, we expand the type IV-C catalog, identifying two phylogenetically distinct clades primarily found in archaea (IV-C1) or bacteria (IV-C2), distinguishable by the Cas10IVc subunit architecture. We functionally and structurally characterize type IV-C1 systems from Thermococcus onnurineus (Ton) and Pyrococcus abyssi (Pab). Type IV-C complexes assemble with crRNAs derived from distinct CRISPR arrays and recognize a 5'-GGG-3' protospacer adjacent motif (PAM) to bind double-stranded DNA targets. Target recognition activates the HD domain of Cas10IVc, triggering metal-dependent collateral cleavage of single-stranded DNA and RNA. This behavior is explained by allosteric alignment of the HD active site, triggered by PAM-dependent R-loop formation, as revealed by cryo-EM. Together, our findings suggest that type IV-C systems provide immunity via non-specific cleavage of nucleic acids generated during mobile genetic element replication or transcription.},
}

@article {pmid42700448,
year = {2026},
author = {Allehyani, N and Alissa, M and Alghamdi, A and Alshehri, MA and Abusalim, GS and Alhegaili, AS and Juraybi, TN and Alsuwat, MA},
title = {CRISPR-Engineered CAR-T Cell Therapy for Epstein-Barr Virus-Associated Nasopharyngeal Carcinoma: A Review of Emerging Therapeutic Prospects.},
journal = {Reviews in medical virology},
volume = {36},
number = {5},
pages = {e70199},
pmid = {42700448},
issn = {1099-1654},
support = {PSAU/2026/R/1448//Prince Sattam bin Abdulaziz University/ ; },
mesh = {Humans ; *Immunotherapy, Adoptive/methods ; *Herpesvirus 4, Human/immunology/physiology ; *Nasopharyngeal Carcinoma/therapy/virology/immunology ; *Epstein-Barr Virus Infections/complications/virology/immunology/therapy ; *CRISPR-Cas Systems ; *Receptors, Chimeric Antigen/genetics/immunology ; Gene Editing ; *Nasopharyngeal Neoplasms/therapy ; Tumor Microenvironment ; },
abstract = {Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) remains a clinically challenging malignancy, particularly in recurrent or metastatic disease where durable responses to chemoradiotherapy and immune checkpoint blockade are limited. The viral aetiology of NPC provides a strong biological rationale for immune-based treatment; however, translation of chimaeric antigen receptor (CAR) T-cell therapy into this solid tumour setting is constrained by poor tumour trafficking, antigen heterogeneity, limited surface accessibility of EBV latent antigens, T-cell exhaustion, and an immunosuppressive tumour microenvironment. This review critically evaluates the emerging therapeutic prospects of CRISPR-engineered CAR-T cell therapy for EBV-associated NPC. It synthesises evidence on EBV latency biology, NPC immune evasion, solid-tumour CAR-T limitations, and genome-engineering strategies including conventional CRISPR-Cas9, base editing, prime editing, and double-strand-break-sparing targeted integration. Particular attention is given to genotoxicity, chromosomal rearrangements, chromosome loss, bystander and off-target editing, manufacturing heterogeneity, and the regulatory and biological barriers that currently separate technical feasibility from NPC-specific clinical implementation. Available clinical evidence from checkpoint blockade, EBV-specific adoptive T-cell therapy, base-edited CAR-T cells in haematologic malignancy, and early CRISPR-edited T-cell trials supports the feasibility of immune and genetic redirection but does not establish efficacy of a clinically validated CRISPR-engineered CAR-T platform for NPC. Future development should prioritise surface-accessible antigen validation, fit-for-purpose selection of editing technology, genomic safety, scalable manufacturing, and biomarker-driven early-phase trials.},
}

Humans
*Immunotherapy, Adoptive/methods
*Herpesvirus 4, Human/immunology/physiology
*Nasopharyngeal Carcinoma/therapy/virology/immunology
*Epstein-Barr Virus Infections/complications/virology/immunology/therapy
*CRISPR-Cas Systems
*Receptors, Chimeric Antigen/genetics/immunology
Gene Editing
*Nasopharyngeal Neoplasms/therapy
Tumor Microenvironment

@article {pmid42700480,
year = {2026},
author = {He, R and Miao, L and Deng, R and Xia, X},
title = {Advances in cascaded CRISPR for preamplification-free nucleic acid assays.},
journal = {Biosensors & bioelectronics},
volume = {314},
number = {},
pages = {119197},
doi = {10.1016/j.bios.2026.119197},
pmid = {42700480},
issn = {1873-4235},
abstract = {The development of rapid, sensitive, and specific nucleic acid assays is pivotal for advancing molecular detection in clinical diagnosis, food safety, and environmental monitoring. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems, renowned for their programmable and signal amplification capacity, have emerged as efficient tools for meeting these challenges. However, the intrinsic sensitivity of CRISPR/Cas assays relying on a single Cas effector is typically confined to the picomolar level, often necessitating complex nucleic acid preamplification. Cascaded CRISPR systems, which integrate sequential enzymatic reactions or multiple CRISPR effectors, can address this limitation by achieving nucleic acid preamplification-free signal enhancement. This review starts with the introduction of the design principles and working mechanisms of cascaded CRISPR strategies, encompassing Enzyme-Coupled cascades, Multi-effector class 2 CRISPR cascades, and Type III CRISPR-mediated cascades. Then, we highlight the deployment of these techniques across diverse bio-sensing scenarios, ranging from disease diagnosis to food and environmental surveillance. Finally, critical challenges and emerging frontiers are discussed, including integration with digital detection platforms and AI-assistant algorithms.},
}

@article {pmid42700916,
year = {2026},
author = {Zhang, X and Zhang, L and Guo, T and Du, W and Wang, S and Li, Y},
title = {Application of emerging technologies in the antiviral field.},
journal = {Antiviral research},
volume = {255},
number = {},
pages = {106529},
doi = {10.1016/j.antiviral.2026.106529},
pmid = {42700916},
issn = {1872-9096},
abstract = {Viral diseases pose a serious threat to global public health, agriculture, and biosecurity. Conventional antiviral strategies are often limited by an incomplete understanding of disease mechanisms, poor targeting precision, and slow response times. Emerging technologies are now reshaping the landscape of antiviral research. This review examines the roles of four key frontiers, including organoid models, gene editing, AI-driven molecular design, and synthetic biology. Organoids provide physiologically relevant platforms that model virus-host interactions and disease progression. Viral infections remain a major challenge to human and animal health, agriculture, and biosecurity. Progress in antiviral research is constrained by the complexity of viral pathogenesis, the diversity and rapid evolution of viruses, and the limited translational relevance of some traditional model systems. Recent advances in organoid technology, gene editing, artificial intelligence, and synthetic biology are expanding the toolkit available for antiviral research and development. In this review, we discuss how these four technological frontiers contribute to disease modeling, target discovery, molecular design, and translational innovation. Organoids, in particular, provide physiologically relevant systems for investigating viral infection, tissue tropism, host responses, and pathogenesis. Gene editing tools, such as CRISPR, enable precise manipulation of host and viral genomes, facilitating the development of resistant organisms and next-generation vaccine platforms. AI technologies, including AlphaFold for structure prediction and platforms for de novo protein design, address long-standing bottlenecks in structural biology and offer powerful means to engineer antiviral proteins, antibodies, and vaccine antigens. Synthetic biology, guided by the Design-Build-Test-Learn cycle, integrates computational design, genetic assembly, and functional validation into a cohesive pipeline. Together, these technologies form a synergistic workflow that spans disease modeling, target discovery, molecular design, construction, testing, and iterative optimization. This integrated approach is shifting antiviral development from traditional empirical methods toward more precise, intelligent strategies. The review also highlights ongoing challenges in integration and scalability, stressing that high-quality biological datasets and stronger interdisciplinary collaboration are essential for realizing translational potential. By presenting a cohesive view of these converging methodologies, this review offers a framework to guide the intelligent evolution of antiviral strategies in both human and animal health.},
}

@article {pmid42702425,
year = {2026},
author = {Li, J and Yuan, M and Cui, X and Ding, Y and Yang, M and Liu, R and Li, L},
title = {A cascaded signal amplification strategy combining Au@Cu2O core-shell nanozymes and CRISPR-Cas12a self-cycling for ultrasensitive colorimetric detection of miRNA-21.},
journal = {Analytica chimica acta},
volume = {1421},
number = {},
pages = {345987},
doi = {10.1016/j.aca.2026.345987},
pmid = {42702425},
issn = {1873-4324},
mesh = {*MicroRNAs/blood/analysis ; *Colorimetry/methods ; *Copper/chemistry ; *Gold/chemistry ; Humans ; *CRISPR-Cas Systems ; Limit of Detection ; },
abstract = {As a critical biomarker for early-stage tumor diagnosis, miRNA-21 poses significant challenges for colorimetric detection due to its ultra-low physiological abundance and high sequence homology. In this study, a multi-stage cascade amplification sensing platform was engineered by integrating an entropy-driven molecular circuit with a heterogeneous nanozyme catalytic network. The platform utilizes Catalytic Hairpin Assembly (CHA) for initial signal transduction, coupled with a CRISPR-Cas12a positive feedback self-cycling system to achieve exponential signal amplification. At the signal output interface, Au@Cu2O core-shell nanocomposites, synthesized via epitaxial growth, exhibit significantly enhanced peroxidase-like activity through interfacial electronic coupling. Experimental results demonstrate a limit of detection (LOD) as low as 1.39 fM, with the capacity to precisely discriminate between serum samples from lung cancer patients and healthy individuals.},
}

*MicroRNAs/blood/analysis
*Colorimetry/methods
*Copper/chemistry
*Gold/chemistry
Humans
*CRISPR-Cas Systems
Limit of Detection

@article {pmid42702653,
year = {2026},
author = {Hu, S and Liu, J and Deng, J and Yuan, Y and Peng, S and Le, M and Li, J and Xu, K},
title = {Recent advances in CRISPR/Cas12a-based biosensors for heavy metal analysis: a review of signal readout strategies and analytical performance.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {42702653},
issn = {1618-2650},
support = {GZC20261162//the China Postdoctoral Science Foundation/ ; 82173572//the National Natural Science Foundation of China/ ; 82574159//the National Natural Science Foundation of China/ ; 2023JJ30430//the Science and Technology Program of Hunan Province/ ; 2026JJ80902//the Science and Technology Program of Hunan Province/ ; 2026JK2006//the Science and Technology Program of Hunan Province/ ; 23A0075//the Department of Education of Hunan Province/ ; },
abstract = {Heavy metals are environmental hazards owing to their toxicity, persistence, and bioaccumulation in living organisms. These metals often accumulate or transform into more toxic compounds, and some accumulate in the human body through the food chain, which is extremely harmful to health. Although conventional detection methods are reliable, they are often hampered by high costs and complex operations, motivating the exploration of alternative sensing strategies. CRISPR/Cas (Clustering Regularly Interspaced Short Palindromic Repeats and Related Proteins) systems have shown potential for developing sensitive assays with significant target specificity, programmability, and signal amplification capabilities. This review discusses research progress on using CRISPR/Cas12a to detect and prevent heavy metal contamination in food. This review introduces methodological innovations in various signal readout methods, including fluorescence, colorimetry, electrochemistry, and microfluidics, and critically evaluates their analytical performance, such as sensitivity, selectivity, and practical applicability in complex food matrices. Finally, this review aims to provide valuable guidance for researchers to develop next-generation diagnostic tools that meet the requirements of rapid screening and precision testing for food safety.},
}

@article {pmid42703025,
year = {2026},
author = {Li, B and Liu, L and Jin, K and Huang, Z and Zhang, T and Gao, R and Chen, H and Niu, L and Fan, C and Zhang, H and Huang, P and Wang, H},
title = {One-Pot RPA-CRISPR/Cas12a Assay With Visual Readout for the Ultra-Specific Detection of Monkeypox Virus Clade I.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70437},
pmid = {42703025},
issn = {1751-7915},
support = {2021YFF0703600//National Key Research and Development Program of China/ ; 20250203114SF//the science and technology development program of Jilin Province/ ; },
mesh = {*CRISPR-Cas Systems ; *Monkeypox virus/genetics/isolation & purification/classification ; *Nucleic Acid Amplification Techniques/methods ; *Mpox, Monkeypox/diagnosis/virology ; Recombinases/metabolism ; Sensitivity and Specificity ; Rapid Diagnostic Tests ; Humans ; Animals ; Limit of Detection ; },
abstract = {In 2024, Monkeypox virus (MPXV) clade I has triggered outbreaks in several countries world-wide. MPXV clade I demonstrates enhanced virulence and transmissibility, with a case fatality rate reaching 10%. In response, we have developed a one-pot detection assay specifically targeting MPXV clade I, combining recombinase polymerase amplification (RPA) and the CRISPR/Cas12a system. The assay can be completed within 40 min and achieved a 95% limit of detection (LOD95) of 27.16 copies/μL. No cross-reactivity was observed with MPXV clade II or other tested viral templates, including Vaccinia virus (Tiantan strain). A preliminary room-temperature evaluation showed that the assay retained detectable performance at 25°C, supporting its potential use in equipment-limited settings. The assay also showed good intra-assay and inter-assay repeatability for recombinant plasmid templates, with all coefficient of variation (CV) values below 10%. In simulated clinical samples, the RPA-CRISPR/Cas12a assay detected more low-concentration plasmid-spiked samples than quantitative polymerase chain reaction (qPCR). These results indicate that the established assay is specific, sensitive, repeatable, and easy to perform, providing a practical tool for field-based screening and decentralized detection of MPXV clade I.},
}

*CRISPR-Cas Systems
*Monkeypox virus/genetics/isolation & purification/classification
*Nucleic Acid Amplification Techniques/methods
*Mpox, Monkeypox/diagnosis/virology
Recombinases/metabolism
Sensitivity and Specificity
Rapid Diagnostic Tests
Humans
Animals
Limit of Detection

@article {pmid41120666,
year = {2026},
author = {Goudy, L and Ha, A and Borah, AA and Umhoefer, JM and Chow, L and Tran, C and Winters, A and Talbot, A and Hernandez, R and Li, Z and Subramanya, S and Arab, A and Kale, N and Lee, JHJ and Muldoon, JJ and Liu, C and Schmidt, R and Santangelo, P and Carnevale, J and Eyquem, J and Shy, BR and Marson, A and Gilbert, LA},
title = {Integrated epigenetic and genetic programming of primary human T cells.},
journal = {Nature biotechnology},
volume = {44},
number = {9},
pages = {1470-1481},
pmid = {41120666},
issn = {1546-1696},
support = {K08 CA273529/CA/NCI NIH HHS/United States ; L30TR002983//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; UM1HG012660//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2021316455)//National Science Foundation (NSF)/ ; 1K08CA252605-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08CA273529//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *T-Lymphocytes/metabolism/cytology ; *Epigenesis, Genetic/genetics ; CRISPR-Cas Systems/genetics ; Epigenome Editing ; *Gene Editing/methods ; Animals ; Receptors, Chimeric Antigen/genetics ; },
abstract = {Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double-strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Lastly, we successfully combined genetic and epigenetic engineering using orthogonal CRISPR Cas12a-dCas9 systems for targeted chimeric antigen receptor (CAR) knock-in and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR-T cell-mediated in vivo tumor control and survival.},
}

Humans
*T-Lymphocytes/metabolism/cytology
*Epigenesis, Genetic/genetics
CRISPR-Cas Systems/genetics
Epigenome Editing
*Gene Editing/methods
Animals
Receptors, Chimeric Antigen/genetics

@article {pmid42314573,
year = {2026},
author = {Landi, E and van Beusekom, E and Ben-Dor, S and Albert, S and Dickman, MM and LaPointe, VLS and van Bokhoven, H},
title = {Biallelic rescue of CTG18.1 in two Fuchs endothelial corneal dystrophy-derived iPSC lines (SCTCi047-A-2, SCTCi046-A-2) following a two-step gene editing strategy.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104032},
doi = {10.1016/j.scr.2026.104032},
pmid = {42314573},
issn = {1876-7753},
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism ; *Fuchs' Endothelial Dystrophy/genetics/pathology/metabolism ; *Gene Editing/methods ; Cell Line ; CRISPR-Cas Systems/genetics ; *Transcription Factor 4/genetics/metabolism ; *Alleles ; },
abstract = {Fuchs endothelial corneal dystrophy (FECD) is an age-related condition distinguished by the degeneration of the corneal endothelium. An intronic CTG18.1 repeat in the transcription factor 4 (TCF4) gene has been associated with a 78-fold increased risk of developing the disease when at least one copy of the CTG18.1 expands above 50 repeats. Employing patient-derived material, we applied a dual CRISPR/Cas9-mediated editing approach to rescue the expansion. Combining non-homologous end-joining (NHEJ) and homologous direct repair (HDR) events, we generated two FECD-derived [+/+](CTG)8 induced pluripotent stem cell (iPSC) lines, which were then successfully characterized, providing relevant isogenic controls for disease-modelling purposes.},
}

Humans
*Induced Pluripotent Stem Cells/metabolism
*Fuchs' Endothelial Dystrophy/genetics/pathology/metabolism
*Gene Editing/methods
Cell Line
CRISPR-Cas Systems/genetics
*Transcription Factor 4/genetics/metabolism
*Alleles

@article {pmid42349105,
year = {2026},
author = {Hamam-Marawi, G and Papadopoulou, M and Ramachandran, H and Dobner, J and Binder, S and Hildebrandt, B and Krutmann, J and Rossi, A},
title = {CRISPR/Cas9-mediated editing of ERCC6 in iPSCs: A disease model for Cockayne Syndrome type B.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104044},
doi = {10.1016/j.scr.2026.104044},
pmid = {42349105},
issn = {1876-7753},
mesh = {Humans ; Poly-ADP-Ribose Binding Proteins/genetics ; *Cockayne Syndrome/genetics/pathology/metabolism ; *DNA Helicases/genetics/metabolism ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *DNA Repair Enzymes/genetics/metabolism ; *CRISPR-Cas Systems/genetics ; Cell Line ; Base Sequence ; Cell Differentiation ; Excision Repair ; },
abstract = {Cockayne Syndrome type B (CSB) is caused by mutations in the ERCC6 gene, which encodes a key protein involved in transcription-coupled nucleotide excision repair (TC-NER) and chromatin remodeling. Deficiency in CSB leads to defective transcriptional recovery after DNA damage, oxidative stress accumulation, and progressive neurodegeneration. In this work, we generated a CRISPR/Cas9-engineered human induced pluripotent stem cell (iPSC) line, IUFi004-A-12, carrying a homozygous mutation in ERCC6 causing a premature stop codon in its 10th exon. The modified iPSCs displayed normal morphology, expressed pluripotency markers, and differentiated into all three germ layers. This model enables mechanistic studies of CSB dysfunction and facilitates therapeutic development for Cockayne Syndrome.},
}

Humans
Poly-ADP-Ribose Binding Proteins/genetics
*Cockayne Syndrome/genetics/pathology/metabolism
*DNA Helicases/genetics/metabolism
*Induced Pluripotent Stem Cells/metabolism/cytology
*DNA Repair Enzymes/genetics/metabolism
*CRISPR-Cas Systems/genetics
Cell Line
Base Sequence
Cell Differentiation
Excision Repair

@article {pmid42361764,
year = {2026},
author = {Liu, NN and Baljinnyam, E and Hu, R and Salemi, SE and Webb, BD and Marro, SG},
title = {Dual CRISPR/Cas9 correction of compound heterozygous MARS2 mutations in the iPSC line ISMMSi060-A from a patient with COXPD25.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104041},
doi = {10.1016/j.scr.2026.104041},
pmid = {42361764},
issn = {1876-7753},
support = {R21 NS130319/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *CRISPR-Cas Systems/genetics ; *Mutation/genetics ; Heterozygote ; Cell Line ; *Mitochondrial Proteins/genetics ; Base Sequence ; Cell Differentiation ; },
abstract = {We previously described the induced pluripotent stem cell (iPSC) line ISMMSi060-A derived from a patient with Combined Oxidative Phosphorylation Deficiency 25 (COXPD25) carrying compound heterozygous pathogenic variants in the mitochondrial methionyl-tRNA synthetase gene, MARS2. Here, we report the generation of the isogenic control line ISMMSi060-A-1 by CRISPR/Cas9-mediated correction of the MARS2 variants c.424C>T (p.Arg142Trp) and c.550C>T (p.Gln184*). The corrected line retained normal morphology, pluripotency, genomic integrity, and differentiation capacity, providing a valuable resource to study MARS2-related mitochondrial dysfunction and therapeutic strategies for COXPD25.},
}

Humans
*Induced Pluripotent Stem Cells/metabolism/cytology
*CRISPR-Cas Systems/genetics
*Mutation/genetics
Heterozygote
Cell Line
*Mitochondrial Proteins/genetics
Base Sequence
Cell Differentiation

@article {pmid42361765,
year = {2026},
author = {Fan, J and Zhang, S and Sun, H and Sun, M and Gu, X and He, Y},
title = {Generation of a FRMD5 knockout human embryonic stem cell line by CRISPR/Cas9 editing.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104048},
doi = {10.1016/j.scr.2026.104048},
pmid = {42361765},
issn = {1876-7753},
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Human Embryonic Stem Cells/metabolism/cytology ; Cell Line ; *Gene Editing/methods ; *Membrane Proteins/genetics/metabolism ; *Gene Knockout Techniques ; Cell Differentiation ; },
abstract = {FRMD5 is a protein-coding gene on human chromosome 15q15.3 encoding a FERM domain-containing protein. Its mutations are linked to NEDEMA, a rare autosomal dominant neurodevelopmental disorder characterized by developmental delay, intellectual disability, ataxia, epilepsy, and eye movement abnormalities (Keller Sarmiento et al., 2024).We established a FRMD5 knockout (FRMD5[-]/[-]) human embryonic stem cell line via CRISPR/Cas9. This line shows normal karyotype, expresses pluripotency markers, and differentiates into three germ layers, serving as a valuable tool for studying FRMD5 in neural development.},
}

Humans
*CRISPR-Cas Systems/genetics
*Human Embryonic Stem Cells/metabolism/cytology
Cell Line
*Gene Editing/methods
*Membrane Proteins/genetics/metabolism
*Gene Knockout Techniques
Cell Differentiation

@article {pmid42378908,
year = {2026},
author = {Lorthongpanich, C and Srisook, P and Jiamvoraphong, N and Klaihmon, P and Kumsui, S and Laowtammathron, C and Issaragrisil, S},
title = {A human iPSC model with LATS1/2 knockdown (MUSIi012-A-9) for investigating Hippo signaling in stem cell.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104052},
doi = {10.1016/j.scr.2026.104052},
pmid = {42378908},
issn = {1876-7753},
mesh = {Humans ; *Protein Serine-Threonine Kinases/metabolism/genetics ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Signal Transduction ; *Tumor Suppressor Proteins/genetics/metabolism ; Cell Differentiation ; Hippo Signaling Pathway ; Gene Knockdown Techniques ; Cell Line ; CRISPR-Cas Systems ; },
abstract = {This study reports the generation and comprehensive characterization of the LATS1/2 knockdown (KD) induced pluripotent stem cell (iPSC) line, MUSIi012-A-9. Created via CRISPR/Cas9-mediated modification of the LATS2 gene in a parental LATS1-KD line, this resource serves as a crucial human model to investigate the roles of LATS1/2 kinases, key regulators of the Hippo signaling pathway. Comprehensive validation confirmed normal iPSC morphology, pluripotency marker expression (OCT3/4, NANOG, SOX2), genetic stability (46,XX karyotype), and robust multilineage differentiation potential. This well-characterized iPSC line is a vital tool for advancing research into Hippo pathway regulation, lineage specification, and cell fate determination in development and disease.},
}

Humans
*Protein Serine-Threonine Kinases/metabolism/genetics
*Induced Pluripotent Stem Cells/metabolism/cytology
*Signal Transduction
*Tumor Suppressor Proteins/genetics/metabolism
Cell Differentiation
Hippo Signaling Pathway
Gene Knockdown Techniques
Cell Line
CRISPR-Cas Systems

@article {pmid42385351,
year = {2026},
author = {Buchmann, S and Aldinger, A and Klopocki, E and Gerull, B},
title = {Establishment of CRISPR/Cas9-edited LEMD2 knock-in (UKWCHFi001-B-1) and knock-out (UKWCHFi001-B-2) iPSC lines to investigate the mechanisms of LEMD2-associated cardiomyopathy.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104049},
doi = {10.1016/j.scr.2026.104049},
pmid = {42385351},
issn = {1876-7753},
mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Membrane Proteins/genetics/metabolism ; *Cardiomyopathies/genetics/metabolism/pathology ; Cell Line ; Gene Knockout Techniques ; *Nuclear Proteins/genetics/metabolism ; *Gene Editing ; Cell Differentiation ; *Gene Knock-In Techniques ; },
abstract = {LEMD2 is an inner nuclear membrane protein. The pathogenic LEMD2 variant (NM_181336.4: c.38 T > G, p.L13R) has been associated with an inherited cardiomyopathy characterized by left ventricular dysfunction and severe arrhythmias. To gain more insights into this disease and investigate the role of LEMD2 more broadly, LEMD2 p.L13R knock-in (LEMD2-KI; UKWCHFi001-B-1) and knock-out (LEMD2-KO; UKWCHFi001-B-2) iPSC lines were generated in a healthy control iPSC (UKWCHFi001-B) line using CRISPR/Cas9 gene editing. Both new iPSC lines retained pluripotency, normal karyotypes, and differentiation potential, whereby expression of LEMD2 was successfully disrupted in LEMD2-KO cells. Thus, these lines provide a suitable model for analyzing LEMD2-associated diseases.},
}

Humans
*CRISPR-Cas Systems/genetics
*Induced Pluripotent Stem Cells/metabolism/cytology
*Membrane Proteins/genetics/metabolism
*Cardiomyopathies/genetics/metabolism/pathology
Cell Line
Gene Knockout Techniques
*Nuclear Proteins/genetics/metabolism
*Gene Editing
Cell Differentiation
*Gene Knock-In Techniques

@article {pmid42391322,
year = {2026},
author = {Wiesbeck, M and Alard, EL and Merino, F and Chowdhury, N and Egert, L and Danese, A and Imhof, S and Iraci Borgia, M and Rajan, A and Fernandez-Novel Marx, N and Kepesidis, E and Köferle, A and Cerron-Alvan, LM and Vierl, F and Truong, TT and Thorwirth, M and Bilalli, L and Santos Dias Mourão, A and Ninkovic, J and Schieweck, R and Diefenbacher, M and Hauck, SM and Trainor, PA and Mardakheh, FK and Götz, M and Stricker, SH},
title = {Manipulation of protein translation and stem cell self-renewal by CRISPR activation of rRNA transcription.},
journal = {Science (New York, N.Y.)},
volume = {393},
number = {6816},
pages = {eaeh1348},
doi = {10.1126/science.aeh1348},
pmid = {42391322},
issn = {1095-9203},
mesh = {*Protein Biosynthesis/genetics ; *RNA, Ribosomal/genetics ; Animals ; *Transcription, Genetic ; *Neural Stem Cells/cytology/metabolism/physiology ; *Cell Self Renewal/genetics ; Cell Proliferation ; Humans ; Mice ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Cell Nucleolus/metabolism ; },
abstract = {Ribosomal RNA (rRNA) transcription rates vary during development, and their dysregulation is linked to diseases such as cancer and ribosomopathies. Owing to their high abundance and genomic redundancy, the functional significance of rRNA levels remains unclear. We developed TAPIR (Targeted Activation of Protein Translation), a CRISPR-based approach to elevate rRNA levels by inducing 47S ribosomal DNA transcription. TAPIR increased nucleolar size and enhanced protein synthesis, even in rapidly proliferating cells. In neural stem cells, elevated translation promoted self-renewal and proliferation in vitro and in vivo. Furthermore, TAPIR enabled the modeling and partial rescue of associated disease phenotypes. Our findings reveal that rRNA levels directly regulate translational output and that protein synthesis capacity can act as a key determinant of mammalian stem cell behavior.},
}

*Protein Biosynthesis/genetics
*RNA, Ribosomal/genetics
Animals
*Transcription, Genetic
*Neural Stem Cells/cytology/metabolism/physiology
*Cell Self Renewal/genetics
Cell Proliferation
Humans
Mice
*CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
Cell Nucleolus/metabolism

@article {pmid42447733,
year = {2026},
author = {Ntzani, ER and Ramachandran, H and Papadopoulou, M and Binder, S and Hildebrandt, B and Haarmann-Stemmann, T and Rossi, A},
title = {CRISPR/Cpf1-mediated knockout of FLG in human induced pluripotent stem cells generates a model for studying epidermal barrier dysfunction.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104056},
doi = {10.1016/j.scr.2026.104056},
pmid = {42447733},
issn = {1876-7753},
mesh = {Humans ; Filaggrin Proteins ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *CRISPR-Cas Systems/genetics ; Cell Differentiation ; *Epidermis/metabolism/pathology ; *Gene Knockout Techniques ; Cell Line ; *Intermediate Filament Proteins/genetics/metabolism ; },
abstract = {Loss of filaggrin (FLG) function impairs skin barrier formation and contributes to common inflammatory skin diseases. In this study, we established a FLG knockout human induced pluripotent stem cell (iPSC) line based on KOLF2.1 J using CRISPR/Cas12a (Cpf1)-mediated genome editing. A guide RNA targeting exon 2 introduced a homozygous mutation, which was confirmed by sequencing. The edited cells maintained typical pluripotent stem cell morphology, expressed key undifferentiated markers, and retained the ability to differentiate into all three germ layers. Karyotype and copy number variation (CNV) analyses confirmed genomic stability and parental origin; the cells were free of mycoplasma. This cell line enables studies of FLG-associated skin biology and pathology.},
}

Humans
Filaggrin Proteins
*Induced Pluripotent Stem Cells/metabolism/cytology
*CRISPR-Cas Systems/genetics
Cell Differentiation
*Epidermis/metabolism/pathology
*Gene Knockout Techniques
Cell Line
*Intermediate Filament Proteins/genetics/metabolism

@article {pmid42470827,
year = {2026},
author = {Dong, Q and Luo, S and Sun, J and Liu, H},
title = {Generation of FCGR3A-EGFP knock-in reporter human embryonic stem cell line, WAe001-A-3S, using CRISPR/Cas9n-based gene targeting.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104061},
doi = {10.1016/j.scr.2026.104061},
pmid = {42470827},
issn = {1876-7753},
mesh = {Humans ; *Receptors, IgG/genetics/metabolism ; *Green Fluorescent Proteins/metabolism/genetics ; *CRISPR-Cas Systems/genetics ; *Human Embryonic Stem Cells/metabolism/cytology ; *Gene Knock-In Techniques ; Cell Differentiation ; Cell Line ; *Gene Targeting ; Genes, Reporter ; },
abstract = {Fc gamma receptor IIIA (FCGR3A) encodes CD16a, a key mediator of antibody-dependent cellular cytotoxicity (ADCC) that regulates innate and adaptive immunity, especially in natural killer (NK) cells and monocytes. We generated an FCGR3A-EGFP knock-in human embryonic stem cell (hESC) line via CRISPR/Casn9n. The cell line showed a normal karyotype, maintained expression ofthe pluripotency markers OCT4, SOX2, and NANOG, and retained trilineage differentiation potential. This reporter line enables real-time tracking of FCGR3A expression during immune cell differentiation, serving as a useful tool for studying FCGR3A[+] immune cell development and related immune mechanisms.},
}

Humans
*Receptors, IgG/genetics/metabolism
*Green Fluorescent Proteins/metabolism/genetics
*CRISPR-Cas Systems/genetics
*Human Embryonic Stem Cells/metabolism/cytology
*Gene Knock-In Techniques
Cell Differentiation
Cell Line
*Gene Targeting
Genes, Reporter

@article {pmid42492408,
year = {2026},
author = {Duan, C and Sun, X and Ding, C and Mao, S and Liang, Y and Liang, Y and Zhang, R and Chen, H and Chen, J and Tang, S},
title = {Generation of a human iPSC line (CSUASOi016-A) modeling X-linked retinoschisis by introducing the RS1 c.214G>A mutation using CRISPR/Cas9.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104060},
doi = {10.1016/j.scr.2026.104060},
pmid = {42492408},
issn = {1876-7753},
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Retinoschisis/genetics/pathology/metabolism ; *CRISPR-Cas Systems/genetics ; *Eye Proteins/genetics/metabolism ; Cell Line ; Mutation ; Cell Differentiation ; Base Sequence ; },
abstract = {X-linked retinoschisis (XLRS) is an inherited retinal degenerative disease caused by mutations in the RS1 gene, leading to visual impairment. The RS1 c.214G>A mutation is a clinically relevant variant associated with XLRS. In this study, we generated a human induced pluripotent stem cell (iPSC) line (CSUASOi016-A) carrying the RS1 c.214G>A (p.E72K) mutation using CRISPR/Cas9. The edited iPSC line exhibited typical pluripotent stem cell morphology, expressed pluripotency markers (OCT4, SSEA4, SOX2, and NANOG), and retained the ability to differentiate into all three germ layers. This cell line provides a valuable resource for modeling XLRS pathogenesis and developing therapeutic strategies.},
}

Humans
*Induced Pluripotent Stem Cells/metabolism/cytology
*Retinoschisis/genetics/pathology/metabolism
*CRISPR-Cas Systems/genetics
*Eye Proteins/genetics/metabolism
Cell Line
Mutation
Cell Differentiation
Base Sequence

@article {pmid42508498,
year = {2026},
author = {Liu, J and Bian, Z and Chen, J and Kang, H and Li, Q and Lin, J and Gou, H and Li, C},
title = {Rapid and visual detection of Lawsonia intracellularis via an RPA-CRISPR/Cas12a assay.},
journal = {Journal of microbiological methods},
volume = {249},
number = {},
pages = {107645},
doi = {10.1016/j.mimet.2026.107645},
pmid = {42508498},
issn = {1872-8359},
mesh = {*Lawsonia Bacteria/isolation & purification/genetics ; Animals ; *Desulfovibrionaceae Infections/diagnosis/veterinary/microbiology ; Swine ; *Swine Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; *CRISPR-Cas Systems ; Rapid Diagnostic Tests ; *Nucleic Acid Amplification Techniques/methods ; Bacterial Proteins/genetics ; },
abstract = {The swine industry faces a substantial economic threat from Lawsonia intracellularis (LI), the bacterium responsible for porcine proliferative enteropathy. Infection commonly presents with diarrhea and increased enterocyte proliferation in the ileum and colon, ultimately resulting in impaired growth performance in affected pigs. Effective management of porcine proliferative enteropathy requires timely and accurate diagnosis. The method provides significant advantages over existing detection techniques, offering enhanced sensitivity and high accuracy. The assay achieves detection within one hour, with no observed cross-reactivity against a panel of common swine pathogens. Results can be visually interpreted under blue light. Clinical validation using 123 samples demonstrated 100% concordance with qPCR results (14 positive and 109 negative). Characterized by simplicity, rapidity, and high sensitivity, the RPA-CRISPR/Cas12a method represents a novel solution for Lawsonia intracellularis detection.},
}

*Lawsonia Bacteria/isolation & purification/genetics
Animals
*Desulfovibrionaceae Infections/diagnosis/veterinary/microbiology
Swine
*Swine Diseases/diagnosis/microbiology
Sensitivity and Specificity
*CRISPR-Cas Systems
Rapid Diagnostic Tests
*Nucleic Acid Amplification Techniques/methods
Bacterial Proteins/genetics

@article {pmid42544618,
year = {2026},
author = {Li, X and Li, D and Wang, Y and Xiang, C and Tan, S and Fan, R and Shi, K and Zhou, W},
title = {HCR-assisted CRISPR/Cas12a platform enables logic-gate and multimodal detection of kanamycin and bisphenol A.},
journal = {Analytical methods : advancing methods and applications},
volume = {18},
number = {34},
pages = {7385-7395},
doi = {10.1039/d6ay01075j},
pmid = {42544618},
issn = {1759-9679},
mesh = {Bisphenol A Compounds ; *Benzhydryl Compounds/analysis ; *Phenols/analysis ; *Biosensing Techniques/methods ; *Kanamycin/analysis ; *CRISPR-Cas Systems/genetics ; Animals ; Nucleic Acid Hybridization/methods ; Milk/chemistry ; Limit of Detection ; Colorimetry/methods ; },
abstract = {A novel triple-modal biosensor integrating hybridization chain reaction (HCR) with CRISPR/Cas12a was developed for sensitive and selective detection of kanamycin (KANA) and bisphenol A (BPA). The system employs a phosphorothioate-modified G-rich hairpin (SHG4-2) as a dual-functional reporter probe, which resists Cas12a trans-cleavage and enables multimodal signal output via SG-quadruplex (SG4) formation. Upon target recognition by aptamers, an initiator strand is released to trigger HCR amplification, generating long double-stranded DNA products that activate Cas12a trans-cleavage. This cleaves the (SHG4-2) probe, releasing SG-rich sequences that self-assemble into SG4 structures, yielding fluorescence (with Thioflavin T), colorimetric (via SG4/hemin-catalyzed TMB oxidation), and smartphone-readable RGB signals. This platform enables parallel detection of a single target analyte, allowing flexible detection modes. Under optimized conditions, the sensor achieved detection limits as low as 20.1 pM for KANA and 6.8 pM for BPA in fluorescence mode, 32.3 pM for KANA and 17.1 pM for BPA in colorimetric mode, and 74.3 pM for KANA and 35.8 pM for BPA in smartphone mode, with excellent selectivity against interfering analogues. Successful application in spiked milk samples demonstrated high recovery rates and good reproducibility. In addition, the platform supports the logical gate operations of OR (single-target detection) and AND (dual-target detection), which allows flexible detection modes. This work presents a versatile, amplification-enhanced multimodal sensing strategy for environmental and food safety monitoring, highlighting its potential for logic-driven biosensing applications.},
}

Bisphenol A Compounds
*Benzhydryl Compounds/analysis
*Phenols/analysis
*Biosensing Techniques/methods
*Kanamycin/analysis
*CRISPR-Cas Systems/genetics
Animals
Nucleic Acid Hybridization/methods
Milk/chemistry
Limit of Detection
Colorimetry/methods

@article {pmid42556251,
year = {2026},
author = {Clémençon, M and Brogard, J and Rozen, M and Hourton, C and Meléndez García, R and Bigou, S and Tsang, SH and Thouvenin, O and Grieve, K and Reichman, S},
title = {Generation of retinitis pigmentosa patient-derived hiPSC lines (IDVi007-A, IDVi007-B) carrying the RHO c.68C > A variant (p.P23H) and CRISPR/Cas9-corrected isogenic hiPSC lines (IDVi007-A-1, IDVi007-A-2, IDVi007-A-3).},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104042},
doi = {10.1016/j.scr.2026.104042},
pmid = {42556251},
issn = {1876-7753},
mesh = {Humans ; *Retinitis Pigmentosa/genetics/pathology/metabolism ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *CRISPR-Cas Systems/genetics ; Cell Line ; Cell Differentiation ; Mutation ; Fibroblasts/metabolism/cytology ; *rho GTP-Binding Proteins/genetics ; },
abstract = {The p.Pro23His (c.68C > A; P23H) mutation leads to autosomal dominant retinitis pigmentosa (adRP). Here, we reprogrammed adRP patient fibroblasts in human induced pluripotent stem cells (hiPSCs) using Sendai virus. We then generated two mutated hiPSC clones and three isogenic controls using CRISPR/Cas9. All five hiPSC lines express pluripotency genes and are able to differentiate into the three germ layers as well as retinal organoids. Altogether, these hiPSCs constitute unique biological tools to elucidate mechanisms of adRP linked to the RHO-P23H mutation.},
}

Humans
*Retinitis Pigmentosa/genetics/pathology/metabolism
*Induced Pluripotent Stem Cells/metabolism/cytology
*CRISPR-Cas Systems/genetics
Cell Line
Cell Differentiation
Mutation
Fibroblasts/metabolism/cytology
*rho GTP-Binding Proteins/genetics

@article {pmid42566814,
year = {2026},
author = {Wang, S and Feng, X and Shang, B and Wang, H and Hu, X and Wang, Z and Li, Z},
title = {Generation of an NKX2-1-EGFP reporter iPSC line with inducible Cas9 for lung progenitor cell tracing.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104072},
doi = {10.1016/j.scr.2026.104072},
pmid = {42566814},
issn = {1876-7753},
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Thyroid Nuclear Factor 1/metabolism/genetics ; *Lung/cytology/metabolism ; *Green Fluorescent Proteins/metabolism/genetics ; CRISPR-Cas Systems/genetics ; Cell Line ; Cell Differentiation ; Genes, Reporter ; },
abstract = {NK2 homeobox 1 (NKX2-1), a master regulator robustly expressed in lung, thyroid, and forebrain, is indispensable for specifying lung epithelial fate and serves as a definitive marker of lung progenitors. Here, we generated a human induced Pluripotent Stem Cell (iPSC) line harboring a doxycycline (dox)-inducible Cas9 and an NKX2-1-EGFP-puro reporter via CRISPR/Cas9-mediated homology-directed repair. This dual-function line combines inducible genome editing with real-time tracing of early lung progenitors, enabling their prospective isolation and screening for stage-specific maturation regulators. Therefore, this engineered iCas9-NKX2-1 EGFP line is a key resource for dissecting human lung development, modeling pulmonary disease, and advancing regenerative therapies.},
}

Humans
*Induced Pluripotent Stem Cells/metabolism/cytology
*Thyroid Nuclear Factor 1/metabolism/genetics
*Lung/cytology/metabolism
*Green Fluorescent Proteins/metabolism/genetics
CRISPR-Cas Systems/genetics
Cell Line
Cell Differentiation
Genes, Reporter

@article {pmid42566815,
year = {2026},
author = {Zhou, H and Li, Y and Jia, M and Du, J and Zheng, K},
title = {CRISPR/Cas9-mediated generation of a homozygous MT4 knockout mouse embryonic stem cell line.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104070},
doi = {10.1016/j.scr.2026.104070},
pmid = {42566815},
issn = {1876-7753},
mesh = {Animals ; *CRISPR-Cas Systems/genetics ; Mice ; *Mouse Embryonic Stem Cells/metabolism/cytology ; Homozygote ; Cell Line ; Mice, Knockout ; Cell Differentiation ; *Metallothionein/genetics/deficiency/metabolism ; Gene Knockout Techniques ; },
abstract = {Metallothionein 4 (MT4) is a low-molecular-weight, cysteine-rich metal-binding protein belonging to the metallothionein family. It exhibits unique skin developmental and differentiation inhibitory activity when functionally impaired and regulates skin cell growth and disease through multiple mechanisms. However, its exact role in cell fate determination remains unknown. Here, we utilized the CRISPR/Cas9 system to generate a homozygous Mt4 knockout (Mt4[-]/[-]) mouse embryonic stem cell (mESC) line. This cell line maintains normal morphology, pluripotency, and the ability to differentiate into all three germ layers. It provides a valuable resource for investigating the mechanisms underlying skin diseases caused by MT4 gene mutations.},
}

Animals
*CRISPR-Cas Systems/genetics
Mice
*Mouse Embryonic Stem Cells/metabolism/cytology
Homozygote
Cell Line
Mice, Knockout
Cell Differentiation
*Metallothionein/genetics/deficiency/metabolism
Gene Knockout Techniques

@article {pmid42615464,
year = {2026},
author = {Kotler, ED and Ashraf, S and Santerre, JP and Kandel, RA},
title = {Optimization of CRISPR dCas9 Lentiviral Transduction in Nucleus Pulposus Cells for Use in Tissue Engineering.},
journal = {Tissue engineering. Part C, Methods},
volume = {32},
number = {8-9},
pages = {310-320},
doi = {10.1177/19373384261477635},
pmid = {42615464},
issn = {1937-3392},
mesh = {Humans ; *Lentivirus/genetics/metabolism ; *Tissue Engineering/methods ; HEK293 Cells ; *Nucleus Pulposus/cytology/metabolism ; *Transduction, Genetic/methods ; *CRISPR-Cas Systems/genetics ; Transfection ; Hepatocyte Nuclear Factor 3-beta/metabolism/genetics ; },
abstract = {Efficient delivery of large gene-editing plasmids, such as the mCherry-CRISPR dCas9 system, into nucleus pulposus (NP) cells is a key step in generating sufficient cells for tissue-engineered intervertebral disc (IVD) constructs and other regenerative therapies for degenerative disc disease (DDD). However, the transfection and transduction of these environmentally sensitive cells remain challenging. This study aimed to identify the best protocol for delivery with minimal cytotoxicity and greatest efficiency. Transfection conditions in HEK293T cells were evaluated using Lipofectamine 3000, Lipofectamine Classic, and ViaFect at different reagent-to-DNA ratios and DNA amounts. Transfection efficiency was quantified by flow cytometry based on mCherry expression. Lentivirus was produced and concentrated by comparing PEG8000, a commercial Lenti-X concentrator, and ultracentrifugation. For NP cell transduction, polybrene and protamine sulfate were tested at multiple concentrations to maximize efficiency and viability. The optimized protocol was validated by delivering a CRISPR/dCas9 Synergistic Activation Mediator (SAM) system to activate endogenous FOXA2, and by seeding the resulting cells onto membranes to assess in vitro NP-like tissue formation. Lipofectamine 3000 at a 2:1 reagent-to-DNA ratio with 0.5 µg DNA per well yielded the highest transfection efficiency in HEK293T cells while minimizing cytotoxicity. Coprecipitation methods for lentiviral concentration, particularly the in-house PEG8000 concentrator, were better than ultracentrifugation. Protamine sulfate at 30 µg/mL yielded efficient NP cell transduction with higher viability than polybrene, as assessed by survival after antibiotic selection. Application of this protocol upregulated endogenous FOXA2 mRNA and protein expression, demonstrating functional efficacy. SAM-FOXA2 cells produced thicker tissue on membrane inserts than SAM controls, confirming compatibility of the protocol with downstream tissue engineering applications. Therefore, an optimized protocol balancing high transfection/transduction efficiency with minimized cytotoxicity was developed, supporting tissue-engineered IVD constructs and other CRISPR-based regenerative therapies for DDD.},
}

Humans
*Lentivirus/genetics/metabolism
*Tissue Engineering/methods
HEK293 Cells
*Nucleus Pulposus/cytology/metabolism
*Transduction, Genetic/methods
*CRISPR-Cas Systems/genetics
Transfection
Hepatocyte Nuclear Factor 3-beta/metabolism/genetics

@article {pmid42624408,
year = {2026},
author = {Zhang, X and Wang, L and Shi, Y and Wang, J and Liu, L and Sun, X and Liang, B and Wang, J and Xu, X},
title = {Development and preliminary evaluation of real-time fluorescence-based RPA and RPA-CRISPR/Cas12a assays for rapid detection of Coxiella burnetii.},
journal = {Journal of microbiological methods},
volume = {249},
number = {},
pages = {107674},
doi = {10.1016/j.mimet.2026.107674},
pmid = {42624408},
issn = {1872-8359},
mesh = {*Coxiella burnetii/genetics/isolation & purification ; Sensitivity and Specificity ; *Q Fever/diagnosis/microbiology ; *CRISPR-Cas Systems ; Humans ; *Nucleic Acid Amplification Techniques/methods ; Rapid Diagnostic Tests ; Animals ; DNA Primers/genetics ; Fluorescence ; DNA, Bacterial/genetics ; },
abstract = {Coxiella burnetii (C. burnetii) is a ubiquitous zoonotic pathogen that exists widely in nature and is an obligate intracellular parasite of eukaryotic cells, causing Q fever in both humans and animals. Therefore, the surveillance and prevention of Q fever are of great importance for public health and the livestock industry. In this study, specific RPA primers, probes, and crRNAs were designed and synthesized targeting the IS1111 gene of C. burnetii, a real-time fluorescence recombinase polymerase amplification (qRPA) assay and a RPA combined with CRISPR/Cas12a (RPA-CRISPR/Cas12a) assay for the rapid detection of C. burnetii were developed. The qRPA assay completed target gene amplification within 20 min, and the amplification curves were monitored in real time on a portable Genie III instrument at 39 °C. The entire single-tube RPA-CRISPR/Cas12a assay, including RPA amplification and CRISPR/Cas12a detection, was completed within 40 min, and the results could be directly visualized under blue-light illumination. Both assays exhibited high specificity for C. burnetii and showed no cross-reactivity with the tested microorganisms. The LOD of the qRPA assay for C. burnetii DNA standard was 54 copies/μL, whereas the LOD of the RPA-CRISPR/Cas12a assay was 1.3 copies/μL. The assays were further evaluated on 456 clinical samples for the detection of C. burnetii. The postive rates of the qRPA and RPA-CRISPR/Cas12a assays were 3.73% (17/456) and 4.17% (19/456), respectively. Compared with qPCR detection results, the concordance rates were 99.34% and 99.78%, respectively. In conclusion, the qRPA and RPA-CRISPR/Cas12a assays developed in this study are rapid, specific and sensitive, making them suitable for the on-site detection of C. burnetii at primary level.},
}

*Coxiella burnetii/genetics/isolation & purification
Sensitivity and Specificity
*Q Fever/diagnosis/microbiology
*CRISPR-Cas Systems
Humans
*Nucleic Acid Amplification Techniques/methods
Rapid Diagnostic Tests
Animals
DNA Primers/genetics
Fluorescence
DNA, Bacterial/genetics

@article {pmid42673729,
year = {2026},
author = {Jones, BM and Xu, M and Zou, J and Liu, C and Zou, Y and Pathak, P and Lomash, RM and Stan, R and Bönnemann, CG and Chen, CZ},
title = {Establishment of induced pluripotent stem cell line TRNDi045-A-38 carrying homozygous DOK7-related Congenital Myasthenia patient-mutation knock-in variant from parental KOLF2.1J.},
journal = {Stem cell research},
volume = {95},
number = {},
pages = {104090},
doi = {10.1016/j.scr.2026.104090},
pmid = {42673729},
issn = {1876-7753},
mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *Myasthenic Syndromes, Congenital/genetics/pathology ; *Muscle Proteins/genetics/metabolism ; Cell Line ; Homozygote ; *Mutation ; Gene Knock-In Techniques ; Female ; CRISPR-Cas Systems ; },
abstract = {DOK7-related Congenital Myasthenic Syndrome (CMS) is a rare genetic neuromuscular junction disorder. This is one of the most common of the recessive forms of CMS, often presenting with more static proximal weakness (hence also referred to as limb girdle CMS). Whole-genome sequencing of affected patients implicates frameshift duplication mutations in DOK7 as drivers of impaired neuromuscular-junction signaling. In this study, we generated a human induced pluripotent stem cell (hiPSC) line TRNDi045-A-38 from the KOLF2.1J reference line, engineered to carry homozygous DOK7 c.1124_1127dupTGCC mutation knock-in using CRISPR/Cas9. This iPSC line could be used for in vitro disease modeling to study disease pathophysiology and for therapeutic development.},
}

Humans
*Induced Pluripotent Stem Cells/metabolism/cytology
*Myasthenic Syndromes, Congenital/genetics/pathology
*Muscle Proteins/genetics/metabolism
Cell Line
Homozygote
*Mutation
Gene Knock-In Techniques
Female
CRISPR-Cas Systems

@article {pmid42696150,
year = {2026},
author = {Sharma, NN and Kumari, A and Vashisht, I and Sharma, MK},
title = {Advances in CRISPR multiplex gene editing to map and modify stress-responsive transcription factor networks for crop improvement.},
journal = {Plant cell reports},
volume = {45},
number = {9},
pages = {},
pmid = {42696150},
issn = {1432-203X},
support = {DST/INSPIRE Fellowship/2021/IF210110//Department of Science and Technology, Ministry of Science and Technology, India/ ; CRG/2023/007038//Anusandhan National Research Foundation,India/ ; ANRF/PAIR/2025/000029/PAIR//JNU-PAIR Network of Anusandhan National Research Foundation, India/ ; },
mesh = {*Gene Editing/methods ; *Transcription Factors/genetics/metabolism ; *Crops, Agricultural/genetics ; *Stress, Physiological/genetics ; *CRISPR-Cas Systems/genetics ; Gene Expression Regulation, Plant ; Plants, Genetically Modified/genetics ; Plant Proteins/genetics/metabolism ; Genome, Plant/genetics ; },
abstract = {The development of CRISPR multiplex genome-editing (MGE) tools is rapidly transforming plant functional genomics and accelerating crop improvements. By simultaneously targeting two or more DNA loci, it allows scientists to precisely edit multiple genes at the single-nucleotide level, within the target genome. Simultaneous manipulation of multiple targets has revolutionized the functional elucidation studies, particularly the dissection of complex genetic pathways. Due to its superior precision and feasibility, CRISPR-MGE is widely accepted and has largely replaced alternative editing tools such as TALENs and ZFNs. Several CRISPR-MGE strategies, including the use of individual expression cassettes, tRNA-processing enzymes, Csy4 or ribozymes, have been successfully deployed in plants. Recent advancements, such as Cpf1, transgene-free methods, or ultra-multiplexing approaches, have further refined the technology into a powerful, efficient, and robust toolkit. MGE enables complex genome editing, including multiple-gene knockouts, base alterations, transcriptional regulation, metabolic engineering, or their combinations. Consequently, it is ideal for elucidating the function of transcription factors that are key molecular players in regulating diverse plant responses, especially in stress pathways. Several stress-responsive TFs have been functionally characterized via CRISPR-MGE, and more advanced tools are being employed. This review evaluates multiplexing tools, their diverse applications, and the current progress toward developing advanced MGE tools. Ultimately, we provide evidence to encourage the use of advanced MGE tools for functional characterization studies of stress-responsive TFs, thereby highlighting their potential to accelerate crop improvement.},
}

*Gene Editing/methods
*Transcription Factors/genetics/metabolism
*Crops, Agricultural/genetics
*Stress, Physiological/genetics
*CRISPR-Cas Systems/genetics
Gene Expression Regulation, Plant
Plants, Genetically Modified/genetics
Plant Proteins/genetics/metabolism
Genome, Plant/genetics

@article {pmid42697642,
year = {2026},
author = {Ye, WN and Xing, Q and Chen, RY and Zhang, YC and Wu, SF and Gao, CF},
title = {Field resistance monitoring and nAChR α6 target validation support spinetoram as a candidate insecticide for rotation in Nilaparvata lugens resistance management.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107264},
doi = {10.1016/j.pestbp.2026.107264},
pmid = {42697642},
issn = {1095-9939},
mesh = {Animals ; *Receptors, Nicotinic/genetics/metabolism ; *Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Hemiptera/drug effects/genetics ; *Macrolides/pharmacology ; *Insect Proteins/genetics/metabolism ; CRISPR-Cas Systems ; Drug Combinations ; },
abstract = {The brown planthopper (BPH), Nilaparvata lugens (Stål), is a major pest threatening rice production in Asia. Severe resistance to commonly used insecticides has become a major challenge for its effective control, highlighting the need for alternative insecticides. In this study, we evaluated the susceptibility of field populations of N. lugens to spinetoram and functionally validated the nicotinic acetylcholine receptor (nAChR) α6 subunit, Nlα6, as a molecular determinant of spinosyn susceptibility. Resistance monitoring showed that field populations remained highly susceptible to spinetoram despite exhibiting moderate to high resistance to several commonly used insecticides. A homozygous Nlα6 knockout strain generated using CRISPR/Cas9 developed high-level resistance to spinosad and spinetoram, with resistance ratios of 554.1 and 357.1, respectively, but did not show broad cross-resistance to nine other nAChR-targeting insecticides. Co-segregation analysis further confirmed tight linkage between Nlα6 loss of function and spinosyn resistance. Inheritance analysis showed that spinetoram resistance mediated by Nlα6 knockout was autosomal and completely recessive. Transcriptome analysis revealed that Nlα6 deficiency was associated with reduced expression of immune defense genes, enrichment of functions related to axonemes and neural processes, and coordinated activation of energy metabolism pathways, suggesting that Nlα6 disruption may alter neural homeostasis and energy demand. These results demonstrate that Nlα6 is a key subunit mediating spinosyn susceptibility in N. lugens and support spinetoram as a candidate rotation insecticide for resistance management.},
}

Animals
*Receptors, Nicotinic/genetics/metabolism
*Insecticide Resistance/genetics
*Insecticides/pharmacology
*Hemiptera/drug effects/genetics
*Macrolides/pharmacology
*Insect Proteins/genetics/metabolism
CRISPR-Cas Systems
Drug Combinations

@article {pmid42697651,
year = {2026},
author = {Zhou, J and Zang, Z and Gao, H and Sun, J and Xu, L and Gao, Q and He, H and Ding, W and Qiu, L and Li, Y},
title = {CRISPR/Cas9-mediated knockout of CsRDL1 decreases the susceptibility of Chilo suppressalis to cyproflanilide.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107282},
doi = {10.1016/j.pestbp.2026.107282},
pmid = {42697651},
issn = {1095-9939},
mesh = {Animals ; *CRISPR-Cas Systems ; *Insecticides/pharmacology ; Gene Knockout Techniques ; Insecticide Resistance/genetics ; *Insect Proteins/genetics/metabolism ; *Moths/drug effects/genetics ; Ivermectin/analogs & derivatives ; Female ; *Anilides/pharmacology ; *Receptors, GABA/genetics ; Larva/drug effects ; },
abstract = {The novel meta-diamide insecticide cyproflanilide represents a promising tool for pest control, yet its precise molecular target remains uncharacterized. The RDL1 encodes a subunit of insect ionotropic GABA receptors (GABAr), which is targeted by meta-diamide pesticides. This study investigated the functional role of the resistance to dieldrin 1 (RDL1) subunit in Chilo suppressalis, a major rice pest, by generating a homozygous CsRDL1 knockout strain (CsRDL1[-/-], lacking 101 bp) via CRISPR/Cas9-mediated gene editing. Bioassay results showed that the CsRDL1[-/-] strain exhibited a 2.67-fold increase in tolerance to cyproflanilide and a 3.08-fold increase to broflanilide, whereas its susceptibility to abamectin and emamectin benzoate, which also act on the CsRDL1 subunit, remained unchanged. These results indicate that knockout of CsRDL1 decreased susceptibility to cyproflanilide and broflanilide, and that the mode of action of these meta-diamides differs from that of abamectin and emamectin benzoate. Meanwhile, the CsRDL1[-/-] strain exhibited significant changes in key biological traits: 3rd-6th instar larval duration shortened by 9.45%, fecundity (eggs per female) reduced by 29.49%, and both pupal duration and female adult longevity were significantly shortened relative to the wild-type population. These findings provide in vivo evidence that CsRDL1 contributes to cyproflanilide susceptibility and plays important roles in development and reproduction in C. suppressalis. This study lays a foundation for further mechanistic studies on the interaction between cyproflanilide and CsRDL1 subunit, and offers insights for the development of insecticides targeting this subunit.},
}

Animals
*CRISPR-Cas Systems
*Insecticides/pharmacology
Gene Knockout Techniques
Insecticide Resistance/genetics
*Insect Proteins/genetics/metabolism
*Moths/drug effects/genetics
Ivermectin/analogs & derivatives
Female
*Anilides/pharmacology
*Receptors, GABA/genetics
Larva/drug effects

@article {pmid42697663,
year = {2026},
author = {Pang, X and Zhang, Z and Qin, D and Bachler, A and Yang, Y and Wu, Y},
title = {Knockout of SfVipR2 confers Vip3Aa resistance in Spodoptera frugiperda with evidence of genetic complementation among non-allelic mutations of SfVipR1, SfVipR2, and SfCHS2.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107294},
doi = {10.1016/j.pestbp.2026.107294},
pmid = {42697663},
issn = {1095-9939},
mesh = {Animals ; *Spodoptera/genetics/drug effects ; *Bacterial Proteins/genetics ; Gene Knockout Techniques ; Mutation ; Genetic Complementation Test ; *Insect Proteins/genetics ; *Insecticide Resistance/genetics ; CRISPR-Cas Systems ; },
abstract = {The Vip3Aa protein from Bacillus thuringiensis is widely deployed in transgenic crops to control lepidopteran pests, including the fall armyworm Spodoptera frugiperda, a highly invasive, polyphagous pest of global importance. Loss-of-function mutations in SfVipR1 (a thyroglobulin-like gene) and SfCHS2 (chitin synthase 2) have previously been confirmed to confer high-level, recessive resistance to Vip3Aa in S. frugiperda. A second thyroglobulin-like gene (HaVipR2) has recently been recognized as an important determinant of Vip3Aa resistance in Helicoverpa armigera. In this study, we first confirmed that knockout of SfVipR2 using CRISPR/Cas9 gene editing also confers high-level, recessive resistance to Vip3Aa. Then, three isogenic knockout strains (SfVipR1-KO established previously; and SfVipR2-KO and SfCHS2-KO, newly generated; all in the YJ-19 genetic background) were used to investigate functional relationships among SfVipR1, SfVipR2, and SfCHS2. Reciprocal crosses between any pair of these resistant strains yielded fully susceptible hybrid progeny, demonstrating complete genetic complementation and no epistasis among the non-allelic mutations. Disruption of any of these genes can result in high-level resistance to Vip3Aa, indicating a substantial resistance risk in S. frugiperda and underscoring the need for resistance management tactics such as establishing an adequate proportion of non-Bt host refuges and deploying pyramided crops expressing Vip proteins and Bt proteins with a different mode of action than Vip3Aa (e.g., Cry proteins).},
}

Animals
*Spodoptera/genetics/drug effects
*Bacterial Proteins/genetics
Gene Knockout Techniques
Mutation
Genetic Complementation Test
*Insect Proteins/genetics
*Insecticide Resistance/genetics
CRISPR-Cas Systems

@article {pmid42697672,
year = {2026},
author = {Kang, R and Qian, Y and Zuo, Y and Li, R and Zhang, L},
title = {Development of an RPA-CRISPR/Cas12a-based rapid visual detection method for two insecticide resistance-associated mutations in Aphis gossypii: A302S in the ace1 gene and M918L in the para gene.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107303},
doi = {10.1016/j.pestbp.2026.107303},
pmid = {42697672},
issn = {1095-9939},
mesh = {Animals ; *Insecticide Resistance/genetics ; Mutation ; *CRISPR-Cas Systems ; Insecticides/pharmacology ; *Insect Proteins/genetics ; },
abstract = {The resistance of Aphis gossypii to pyrethroids and organophosphate/carbamate insecticides has become increasingly severe. The para M918L and ace1 A302S target-site mutations are the key mechanisms conferring resistance to these two types of insecticides, respectively. However, rapid and field-deployable methods for detecting these mutations are still lacking. In this study, the genotype and allele frequencies of eight field populations collected in 2023 were investigated, and a rapid visual detection method based on RPA-CRISPR/Cas12a was developed. By optimizing the concentration of the reaction components, specific recognition of both mutations was achieved. The optimized assay could be completed within 1 h under a single-temperature condition of 37 °C, with fluorescence signals directly visualized using a portable 440-460 nm blue-light illuminator without PCR thermocyclers, fluorescence readers or sequencing platforms. Validation using the tested field samples showed complete concordance with Sanger sequencing. In addition, Sanger sequencing further showed that no homozygous susceptible genotype was detected at the para M918 locus across all populations, whereas the 302S allele frequency at the ace1 A302S locus exhibited significant geographic variation, ranging from 0% to 100%. The RPA-CRISPR-based visual detection method developed in this study is rapid, accurate, and does not require expensive instrumentation. Together with previously developed neonicotinoid resistance detection techniques, it forms a comprehensive monitoring system for multiple resistance in A. gossypii, providing a practical tool for rapid field diagnosis and more informed insecticide selection.},
}

Animals
*Insecticide Resistance/genetics
Mutation
*CRISPR-Cas Systems
Insecticides/pharmacology
*Insect Proteins/genetics

@article {pmid42699674,
year = {2026},
author = {Mohanty, A and Sahoo, RK and Sanket, AS and Rout, E},
title = {Combating New Delhi metallo-beta-lactamase-1 (NDM-1): an integrated review of inhibitor development and next-generation therapeutic platforms.},
journal = {RSC advances},
volume = {},
number = {},
pages = {},
pmid = {42699674},
issn = {2046-2069},
abstract = {New Delhi metallo-β-lactamase-1 (NDM-1), which has emerged globally, exhibits resistance to almost all β-lactam antibiotics, including carbapenems, posing a major challenge to modern antibiotic therapy. Deep sequencing has revealed the evolution of several new NDM variants (some of the variants are more thermostable than NDM-1) due to mutations that increase their zinc-binding and catalytic efficiency and establish a selective pressure on the enzymes. In addition to enzymatic breakdown, NDM-mediated resistance is exorbitantly exhibited via porin loss, efflux pump activity, biofilm formation, and outer membrane vesicle-mediated dissemination. Despite the urgent need for effective countermeasures, no clinically approved inhibitor of NDM-1 has been developed. This review explores the structural and functional characteristics of NDM-1, together with the epidemiology of bla NDM-1-harbouring bacterial pathogens. It further elaborates the catalytic basis of the broad-spectrum β-lactam hydrolysis mechanism, attributed to the presence of dinuclear Zn(ii); the conserved αβ/βα metallo-β-lactamase fold, and flexible active-site loops that govern substrate recognition are also highlighted. In addition, this review provides details on the known inhibitor classes, including thiol-based compounds, hydroxamates, bicyclic boronates, repurposed drugs, and natural products, and discusses the challenges related to pharmacokinetics, toxicity, and variant-specific effectiveness. Other emerging approaches, such as CRISPR-Cas systems for targeted gene editing, nanoparticle-based delivery platforms, and artificial intelligence-driven drug discovery, are also explored as promising options for future therapy development.},
}

@article {pmid42364585,
year = {2027},
author = {Wang, T and Wen, Y and Ma, H and Wang, Y and Liao, K and Xue, F},
title = {RAA-CRISPR/Cas12a-mediated SERS magnetic biosensor combined with a portable Raman spectrometer for rapid and ultrasensitive detection of Lumpy skin disease virus.},
journal = {Talanta},
volume = {311},
number = {},
pages = {130222},
doi = {10.1016/j.talanta.2026.130222},
pmid = {42364585},
issn = {1873-3573},
mesh = {*Biosensing Techniques/methods ; *Spectrum Analysis, Raman/methods ; Animals ; *CRISPR-Cas Systems ; *Lumpy skin disease virus/isolation & purification/genetics ; Cattle ; Nucleic Acid Amplification Techniques/methods ; DNA, Viral/genetics ; Rapid Diagnostic Tests ; Recombinases/metabolism ; Gold/chemistry ; },
abstract = {Lumpy skin disease virus (LSDV) poses a severe threat to global cattle farming, causing significant economic losses. Current laboratory-based methods such as qPCR are accurate procedures; however, they are time-consuming and require sophisticated instrumentation, thus hindering onsite outbreak control. We report a novel magnetic biosensor integrating recombinase-aided amplification (RAA), clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a, and surface-enhanced Raman scattering (SERS) for ultrasensitive and portable detection of LSDV. The biosensor operates through a synergistic cascade: (i) RAA isothermally amplifies the viral DNA target; (ii) the amplified product activates the trans-cleavage activity of CRISPR/Cas12a, thus generating numerous short ssDNA fragments; and (iii) these fragments cleave linker DNA, thereby releasing AuNS@DTNB SERS nanoprobes from the magnetic bead surface and enabling signal readout via a handheld Raman spectrometer. This triple-amplification strategy yielded an ultrahigh sensitivity at 1.2 copies/μL, with a total assay time of only 90 min. The platform exhibited exceptional specificity, discriminating LSDV from genetically homologous Capripoxviruses (up to 97% similarity). In blind tests on 30 beef samples spiked with LSDV nucleic acid, it achieved 100% concordance with qPCR results, thus demonstrating excellent robustness. By integrating a handheld Raman spectrometer and a portable thermostat, this platform delivers laboratory-grade performance in a field-deployable format. This biosensor represents a powerful new tool for onsite LSDV surveillance; given its modular design, it can be readily adapted for detecting other emerging nucleic acid targets.},
}

*Biosensing Techniques/methods
*Spectrum Analysis, Raman/methods
Animals
*CRISPR-Cas Systems
*Lumpy skin disease virus/isolation & purification/genetics
Cattle
Nucleic Acid Amplification Techniques/methods
DNA, Viral/genetics
Rapid Diagnostic Tests
Recombinases/metabolism
Gold/chemistry

@article {pmid42379036,
year = {2027},
author = {Chen, Y and Liu, S and Yuan, Z and He, X and Zhu, X and Wang, G and Wang, X},
title = {Dual-engine amplification: Integrating catalytic hairpin assembly with CRISPR-Cas12a for ultrasensitive point-of-care testing of Chikungunya virus RNA.},
journal = {Talanta},
volume = {311},
number = {},
pages = {130191},
doi = {10.1016/j.talanta.2026.130191},
pmid = {42379036},
issn = {1873-3573},
mesh = {*RNA, Viral/genetics/analysis ; *Chikungunya virus/genetics/isolation & purification ; *Nucleic Acid Amplification Techniques/methods ; *Point-of-Care Testing ; *CRISPR-Cas Systems ; *Biosensing Techniques/methods ; Humans ; *Chikungunya Fever/diagnosis/virology ; Rapid Diagnostic Tests ; Limit of Detection ; Sensitivity and Specificity ; },
abstract = {Chikungunya virus (CHIKV) has emerged as a globally important arthropod-borne pathogen with rapid geographical expansion, urging high-performance yet simple diagnostic tools. Herein, we develop an isothermal dual-engine amplification biosensor by integrating catalytic hairpin assembly (CHA) with CRISPR-Cas12a for ultrasensitive and rapid detection of CHIKV RNA. This strategy combines the enzyme-free isothermal amplification of CHA and the high-specificity trans-cleavage activity of CRISPR-Cas12a to realize cascade signal enhancement. By systematically optimizing reaction parameters including probe ratio, temperature, buffer, and incubation time, we achieve superior analytical performance. The biosensor exhibits a low limit of detection of 4 fM, a wide linear range from 10 fM to 1 μM (R[2] > 0.98), and excellent specificity against dengue virus, Zika virus, and other common blood-borne viruses. It also shows strong resistance to interference from hemolysis, icterus, and lipemia. The whole assay can be finished within 60 min under isothermal conditions without sophisticated thermal cyclers. In clinical serum samples, this method achieves 97.5% concordance with RT-qPCR, with a sensitivity of 96.8% and a specificity of 100%. This CHA-CRISPR-Cas12a dual-amplification platform provides a sensitive, specific, rapid, and cost-effective approach for CHIKV detection and holds great promise for point-of-care testing in resource-limited settings.},
}

*RNA, Viral/genetics/analysis
*Chikungunya virus/genetics/isolation & purification
*Nucleic Acid Amplification Techniques/methods
*Point-of-Care Testing
*CRISPR-Cas Systems
*Biosensing Techniques/methods
Humans
*Chikungunya Fever/diagnosis/virology
Rapid Diagnostic Tests
Limit of Detection
Sensitivity and Specificity

@article {pmid42402225,
year = {2027},
author = {Jia, X and Wang, J},
title = {Aptamer-CRISPR Glucose Transducer for point-of-care IgE detection.},
journal = {Talanta},
volume = {311},
number = {},
pages = {130221},
doi = {10.1016/j.talanta.2026.130221},
pmid = {42402225},
issn = {1873-3573},
mesh = {*Immunoglobulin E/analysis/blood ; Humans ; *Aptamers, Nucleotide/chemistry ; *Biosensing Techniques/methods ; *Point-of-Care Systems ; *Glucose/analysis ; *CRISPR-Cas Systems ; *Point-of-Care Testing ; Limit of Detection ; Rapid Diagnostic Tests ; },
abstract = {Immunoglobulin E (IgE) is a critical biomarker for the diagnosis and therapeutic monitoring of allergic diseases. Conventional IgE detection methods (e.g., ELISA, ImmunoCAP) generally offer satisfactory sensitivity but require hours to days, rely on specialized equipment and trained personnel, and are unsuitable for point-of-care or home-based testing. Here, we developed a portable point-of-care testing platform termed Aptamer-CRISPR Glucose Transducer (ACGT), based on aptamer competition and CRISPR-Cas12a trans-cleavage. The platform employs the D17.4 aptamer as the molecular recognition element. In the presence of target IgE, the aptamer specifically binds IgE, triggering a strand displacement reaction that releases the blocker as ssDNA. This released blocker (now serving as the trigger) activates the trans-cleavage of Cas12a, which cleaves ssDNA linkers on magnetic beads, thereby releasing invertase into the supernatant. The released invertase hydrolyzes sucrose into glucose, which is quantitatively measured using a personal glucose meter. The method achieves a detection limit as low as 76.5 kU/L, with a total assay time of approximately 80 min. By integrating the signal amplification capability of CRISPR with the accessibility of glucose-based transduction, the ACGT platform provides a sensitive, cost-effective, and user-friendly solution for allergen diagnosis and biomarker monitoring in decentralized settings, offering great potential for primary care and home-based testing.},
}

*Immunoglobulin E/analysis/blood
Humans
*Aptamers, Nucleotide/chemistry
*Biosensing Techniques/methods
*Point-of-Care Systems
*Glucose/analysis
*CRISPR-Cas Systems
*Point-of-Care Testing
Limit of Detection
Rapid Diagnostic Tests

@article {pmid42420522,
year = {2026},
author = {Price, D and Zemlyanskiy, G and Trakarnphornsombat, W and Forne, I and Volkova, N and Dubusse, L and Cooper, AJ and Imhof, A and Radzisheuskaya, A},
title = {Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing.},
journal = {Nature genetics},
volume = {58},
number = {9},
pages = {2303-2319},
pmid = {42420522},
issn = {1546-1718},
support = {UKRI698//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; EP/Y000331/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; RG\R1\241175//Royal Society/ ; CRC1309/325871075 and SPP2191/419067076//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Histones/genetics/metabolism/chemistry ; Animals ; *Lysine/genetics/metabolism ; Mice ; *Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Protein Processing, Post-Translational/genetics ; Mouse Embryonic Stem Cells/metabolism ; Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Mutation ; Genomic Instability ; Saccharomyces cerevisiae/genetics ; },
abstract = {Histone post-translational modifications are fundamental to genome regulation, yet dissecting the functions of individual histone marks in mammals remains challenging due to the presence of multiple histone gene copies. Here we develop a high-throughput clustered regularly interspaced short palindromic repeats (CRISPR) prime editing platform enabling precise, reversible and combinatorial mutagenesis of canonical and noncanonical histone H3 genes within their native genomic context. Using systematic lysine-to-arginine substitutions benchmarked against synonymous controls, we identify key residues, including H3K4, H3K9, H3K14, H3K18 and H3K79, whose mutation compromises fitness in mouse embryonic stem cells. We further show that H3K56, linked to genome stability in yeast and Drosophila, has a conserved role in mammalian cells. Through analysis of selected double mutants, we uncover functional crosstalk across residues, with combinations such as H3K27R + H3K36R impairing stem cell self-renewal and altering transcription. Altogether, this study establishes a functional map of histone H3 lysines in mammals and provides a broadly applicable platform for systematic dissection of chromatin regulation.},
}

*Histones/genetics/metabolism/chemistry
Animals
*Lysine/genetics/metabolism
Mice
*Gene Editing/methods
*CRISPR-Cas Systems/genetics
Protein Processing, Post-Translational/genetics
Mouse Embryonic Stem Cells/metabolism
Humans
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Mutation
Genomic Instability
Saccharomyces cerevisiae/genetics

@article {pmid42664856,
year = {2026},
author = {Huang, J and Zhang, Q and Yu, FW and Liu, MQ and Jing, HK and Wang, SY and Wang, HY and Li, JQ and Zheng, L and Shao, H and He, XL and Shen, RF and Zhu, XF},
title = {Disruption of OsGONST3 reduces grain cadmium accumulation without yield penalty in field-grown rice.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143397},
doi = {10.1016/j.jhazmat.2026.143397},
pmid = {42664856},
issn = {1873-3336},
mesh = {*Oryza/metabolism/genetics/growth & development ; *Cadmium/metabolism ; *Plant Proteins/genetics/metabolism ; *Soil Pollutants/metabolism ; Plants, Genetically Modified ; Plant Roots/metabolism ; CRISPR-Cas Systems ; },
abstract = {Cadmium (Cd) pollution in paddy soils threatens global food safety. Identifying molecular gateways controlling grain Cd accumulation is essential for breeding low-Cd rice. A field-based screen of a large-scale CRISPR/Cas9 mutant library identified OsGONST3, a Golgi nucleotide sugar transporter family member localized to the plasma membrane. After 1 μM Cd treatment for 7 d, OsGONST3 transcript abundance increased approximately 3.4-fold in root and 5.7-fold in shoot, accompanied by increased OsGONST3-GFP protein accumulation. Heterologous OsGONST3 expression increased yeast Cd content by approximately 23% relative to the empty-vector control. Under hydroponic exposure to 1 μM Cd for 7 d, two independent osgonst3 mutants contained 22-25% less Cd in root, approximately 13% less in shoot, and 16-21% less in xylem sap than Nipponbare. Conversely, OsGONST3-overexpressing lines contained 40-42%, 38-40%, and 28-37% more Cd in root, shoot, and xylem sap, respectively. Under tested field condition, OsGONST3 disruption reduced grain Cd by approximately 25-26% without a significant yield penalty and was associated with secondary transcriptional adjustments in Cd-homeostasis genes. These findings identify OsGONST3 as a plasma membrane-localized Cd influx-associated protein and a promising target for breeding low-Cd rice.},
}

*Oryza/metabolism/genetics/growth & development
*Cadmium/metabolism
*Plant Proteins/genetics/metabolism
*Soil Pollutants/metabolism
Plants, Genetically Modified
Plant Roots/metabolism
CRISPR-Cas Systems

@article {pmid42690973,
year = {2026},
author = {Qin, Y and Zhang, G and Hu, Y},
title = {CRISPR/Cas- and Argonaute-Based In Vivo Nucleic-Acid Imaging Technologies: Strategies, Challenges, and Perspectives.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.6c01856},
pmid = {42690973},
issn = {2379-3694},
support = {32401261//National Natural Science Foundation of China/ ; },
abstract = {Live-cell monitoring of sequence-specific nucleic acids is essential to understanding genome organization, RNA regulation, and disease progression. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) and Argonaute (Ago) systems provide programmable, guide-directed recognition of DNA or RNA and are increasingly used as platforms for in vivo bioimaging. This review summarizes the structural and mechanistic features of representative CRISPR and Ago effectors and discusses design strategies for sensitive, specific, and multiplexed imaging of genomic loci, extrachromosomal DNA, and endogenous RNA in living cells. We compare the analytical performance and limitations of CRISPR- and Ago-based imaging, with particular emphasis on the major technical and biological challenges affecting their accuracy, applicability, and reliability. Finally, this review offers insights into developing high-resolution and user-friendly bioimaging platforms for fundamental biology and future translational applications.},
}

@article {pmid42692561,
year = {2026},
author = {Zheng, Z and Xu, D},
title = {CRISPR-Cas9 screen to identify genes regulating cell death.},
journal = {Methods in cell biology},
volume = {210},
number = {},
pages = {83-96},
doi = {10.1016/bs.mcb.2026.05.010},
pmid = {42692561},
issn = {0091-679X},
mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *Cell Death/genetics ; Animals ; *Apoptosis/genetics ; },
abstract = {Regulated cell death mediated by dedicated molecular machines, known as programmed cell death, plays important roles in health and disease. Understanding the mechanisms of cell death is crucial for elucidating the control of cellular homeostasis and developing therapies for related diseases. Despite extensive research efforts spanning decades, many aspects of cell death mechanisms remain elusive, highlighting the need for continued exploration. Here, we describe how to identify novel regulators involved in cell death pathways using a genome-wide screening approach.},
}

*CRISPR-Cas Systems/genetics
Humans
*Cell Death/genetics
Animals
*Apoptosis/genetics

@article {pmid42692894,
year = {2026},
author = {Gaizauskaite, U and Songailiene, I and Sasnauskas, G and Siksnys, V},
title = {Building CRISPR immunity: evolution and mechanisms of spacer acquisition.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2026.08.004},
pmid = {42692894},
issn = {0968-0004},
abstract = {CRISPR-Cas systems in prokaryotes serve as adaptive immune systems that neutralize phage infections through RNA-guided nucleases. Immunization is achieved during the adaptation stage through Cas1-Cas2 integrase-mediated insertion of short foreign DNA snippets, termed spacers, into a CRISPR array in the host genome. This review examines the evolutionary origins of Cas1-Cas2 and the mechanisms of spacer acquisition in DNA-targeting CRISPR-Cas systems. Particular emphasis is placed on the recently characterized effector-assisted adaptation pathways, in which CRISPR effector proteins, such as Cascade and Cas9, typically involved in target interference, are repurposed for prespacer capture and integration into a CRISPR array.},
}

@article {pmid42694431,
year = {2026},
author = {Putignani, L and Marsiglia, R and Turco, L and Russo, A and Pane, S and Fusco, A and Lopetuso, L and Trecarichi, EM},
title = {The gut reservoir of carbapenem-resistant Enterobacterales: from dysbiosis and colonization to infection and decolonization, with a focus on patients with hematologic malignancies - a narrative review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1939690},
pmid = {42694431},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications/microbiology ; *Dysbiosis/microbiology ; *Enterobacteriaceae Infections/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Probiotics ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE) remain among the highest-priority antimicrobial-resistant pathogens worldwide, and intestinal colonization is increasingly recognized as the key precursor of invasive infections, particularly in patients with hematological malignancies. Increasing evidence indicates that disruption of the gut microbial ecosystem, reflected in reduced diversity, depletion of beneficial anaerobic taxa, intestinal barrier dysfunction, immune dysregulation, and expansion of Enterobacterales, plays a central role in the transition from colonization to infection. Consequently, restoring colonization resistance through microbiome-targeted interventions has emerged as a promising preventive strategy. This narrative review summarizes the current evidence on the epidemiology and clinical impact of CRE colonization and infection, with particular emphasis on the ecological alterations of the gut microbiome linking gut dysbiosis to epithelial barrier dysfunction, immune dysregulation, and loss of colonization resistance to CRE persistence and invasive infection. We critically discuss both conventional and emerging decolonization approaches, including selective digestive decontamination, probiotics, prebiotics and synbiotics, fecal microbiota transplantation (FMT), bacteriophage therapy, and CRISPR-Cas-based technologies, highlighting their mechanisms of action, available clinical evidence, and current limitations. Particular attention is given to patients with hematological malignancies, in whom the clinical need for effective decolonization strategies is greatest. Although FMT currently represents the most promising microbiome-based intervention, the available evidence remains heterogeneous and largely derived from small studies. Overall, durable and standardized decolonization strategies have yet to be established, underscoring the need for well-designed multicenter randomized clinical trials to define effective microbiome-directed approaches for preventing CRE-related infections in high-risk populations.},
}

Humans
*Hematologic Neoplasms/complications/microbiology
*Dysbiosis/microbiology
*Enterobacteriaceae Infections/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Anti-Bacterial Agents/pharmacology/therapeutic use
Probiotics

@article {pmid42694879,
year = {2026},
author = {Huang, CW and Chen, HH and Jao, TM and Li, CJ and Sung, JM and Tsai, YS and Chen, JS},
title = {CRISPR/Cas9-Driven Fndc5 Knockout Reveals Augmented Mitochondrial Structural and Dynamic Alterations in Diabetic Nephropathy.},
journal = {International journal of medical sciences},
volume = {23},
number = {9},
pages = {2884-2898},
pmid = {42694879},
issn = {1449-1907},
mesh = {Animals ; Mice ; *Diabetic Nephropathies/pathology/genetics ; *Mitochondria/pathology/metabolism/genetics/ultrastructure ; Mice, Knockout ; *Diabetes Mellitus, Experimental/pathology/genetics/chemically induced/complications ; *Fibronectins/genetics/metabolism ; CRISPR-Cas Systems/genetics ; Male ; Diet, High-Fat/adverse effects ; Mitochondrial Dynamics/genetics ; Kidney/pathology ; Mice, Inbred C57BL ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism ; Oxidative Stress/genetics ; Humans ; Streptozocin/toxicity ; Lipid Peroxidation/genetics ; },
abstract = {FNDC5 has been implicated in glucose homeostasis and is associated with mitochondrial function. Its role in diabetes and diabetic nephropathy (DN) remains unclear. This study hypothesizes that FNDC5 deficiency predisposes the kidney to accelerated mitochondrial dysfunction in diabetes and DN. Systemic Fndc5 knockout (KO) C57BL/6 mice were generated using CRISPR/Cas9. DN were induced in six-week-old Fndc5 wild-type (WT) and KO mice using high-fat diet combined with streptozotocin injection. Weekly blood and urine analyses assessed glucose, cholesterol, triglycerides, blood urea nitrogen, creatinine, and proteinuria. At 15 weeks, kidneys and metabolic tissues including pancreas, muscle and adipose were collected for histological and molecular analyses. Results showed that while both Fndc5 WT and KO mice were successfully induced with hyperglycemia, the Fndc5 KO DN group exhibited a slightly lower cumulative glycemic burden compared with the WT DN group. Despite this milder metabolic stress, proteinuria remained comparable between the two groups. Furthermore, histological analysis revealed that Fndc5 KO DN mice displayed more severe mesangial expansion, glomerular basement membrane thickening, and podocyte effacement compared with WT DN mice. The elevated lipid peroxidation, reduced PGC-1α expression, and increased DNA fragmentation were also evident in Fndc5 KO DN. More swollen mitochondria with a significantly higher percentage of disrupted cristae were observed in Fndc5 KO DN mice compared with WT DN mice. This was accompanied by the upregulation of mitochondrial fission-related genes (Dnm1l and Fis1), downregulation of the fusion-related gene (Mfn1), and reduced expression of ATP synthase subunits (ATP5A1 and ATP5B). Systemic analysis of other metabolic tissues, including the pancreas and muscle and adipose tissues, revealed increased lipid peroxidation and decreased PGC-1α expression. These findings underscore FNDC5's role in maintaining mitochondrial integrity and cellular health under diabetic conditions, positioning FNDC5 as a potential therapeutic target.},
}

Animals
Mice
*Diabetic Nephropathies/pathology/genetics
*Mitochondria/pathology/metabolism/genetics/ultrastructure
Mice, Knockout
*Diabetes Mellitus, Experimental/pathology/genetics/chemically induced/complications
*Fibronectins/genetics/metabolism
CRISPR-Cas Systems/genetics
Male
Diet, High-Fat/adverse effects
Mitochondrial Dynamics/genetics
Kidney/pathology
Mice, Inbred C57BL
Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism
Oxidative Stress/genetics
Humans
Streptozocin/toxicity
Lipid Peroxidation/genetics

@article {pmid42695329,
year = {2026},
author = {Chowdhury, S and Nayak, SP and Pattanayak, R and Sardar, S and Majhi, A and Yadav, B and Dasari, A and Mandlik, R and Sonah, H and Deshmukh, R and Gupta, I and Bauer, P and Ram, H},
title = {Establishment of a CRISPR-Cas9 Library for Indica Rice and Identification of OsOPR5 (LOC_Os06g11210) as a Regulator of Root Architecture.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71097},
pmid = {42695329},
issn = {1399-3054},
support = {SRGJ2021/001495//Department of Biotechnology, Ministry of Science and Technology, Govt of India/ ; BT/PR53626/BSA/33/96/2024//Department of Biotechnology, Ministry of Science and Technology, Govt of India/ ; BT/PR56697/AMRIT/165/21/2025//Department of Biotechnology, Ministry of Science and Technology, Govt of India/ ; //BRIC-National Institute of Plant Genome Research/ ; //Alexander von Humboldt Foundation/ ; },
mesh = {*Oryza/genetics/metabolism ; *CRISPR-Cas Systems/genetics ; *Plant Roots/genetics/anatomy & histology/growth & development/metabolism ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Gene Library ; Gene Expression Regulation, Plant ; Mutation ; Cyclopentanes/metabolism ; Oxylipins/metabolism ; Gene Editing ; },
abstract = {Functional characterization of a large number of rice genes remains a major challenge despite the availability of genome sequences and large-scale transcriptomic datasets. CRISPR-Cas9 library is a powerful approach for high-throughput targeted mutagenesis; however, its application in indica rice cultivars remains limited due to low transformation and regeneration efficiencies. In this study, we developed a CRISPR-Cas9 library targeting 12,000 rice genes and evaluated its utility for functional genomics in the indica cultivar MTU-1010. Sanger sequencing and NGS analysis of the plasmid library revealed high sgRNA coverage and more than 80% accuracy. Transformation of the developed library into the indica cultivar MTU-1010 resulted in a high target editing efficiency, with 90% of analyzed transgenic plants carrying mutations at the intended target site. Functional analysis of one homozygous mutant identified a previously uncharacterized role for OsOPR5 (LOC_Os06g11210), a member of the 12-oxophytodienoate reductase family in root architecture. The opr5 mutants exhibited significant reductions in lateral root number, seminal and crown root number, and root length, demonstrating that OsOPR5 positively regulates root system architecture in rice. Notably, endogenous jasmonic acid (JA) and JA-isoleucine levels were not significantly altered in the mutant, suggesting potential functional specialization or redundancy among rice OPR family members for JA accumulation. The root system architecture is a key determinant of water and nutrient acquisition; our results suggest that OsOPR5 may play an important role in adaptation under adverse environmental conditions. Collectively, this study establishes an efficient genome-editing platform for indica rice and identifies OsOPR5 as a novel regulator of root development.},
}

*Oryza/genetics/metabolism
*CRISPR-Cas Systems/genetics
*Plant Roots/genetics/anatomy & histology/growth & development/metabolism
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified
Gene Library
Gene Expression Regulation, Plant
Mutation
Cyclopentanes/metabolism
Oxylipins/metabolism
Gene Editing

@article {pmid42695976,
year = {2026},
author = {de Kreek, F and Hertzberger, R and van Eeden, F and Illidge, S and Teunis, EJ and Hanemaaijer, M and Lievens, E and Rienstra, F and Wiedhaup, DE and Lisotto, P and Butler, D and Molenaar, D and Kort, R},
title = {Intra-individual genetic diversity of vaginal Lactobacillus crispatus revealed through citizen science-driven isolation and pangenome analysis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag218},
pmid = {42695976},
issn = {1365-2672},
abstract = {AIMS: A vaginal microbiome dominated by Lactobacillus crispatus is associated with positive reproductive and sexual health outcomes, yet intra-individual genetic diversity within this species remains largely unexplored. This study characterised inter- and intra-individual genomic variation in L. crispatus strains isolated through a citizen science initiative and assessed implications for multi-strain probiotic development.

METHODS AND RESULTS: Fifty-three women participated in this citizen science project. Self-sampling resulted in 48 shotgun metagenomes. Twenty-two participants isolated their own L. crispatus strains using selective enrichment and LAMP-based species confirmation, resulting in 53 whole-genome-sequenced isolates. L. crispatus dominated 20 of 48 metagenomes (50.1-99.6% relative abundance). Pangenome analysis revealed 3 456 gene families, of which 43.7% were core and 56.3% accessory. A 14-kb plasmid harbouring a Fic-domain toxin-antitoxin protein, but devoid of antimicrobial resistance genes, was present in 44 of 53 strains. Strains from the same individual clustered closely together yet harboured 1-123 gene differences. Intra-individual variation was observed in the pullulanase type I gene required for glycogen degradation: 40 strains were predicted to grow on glycogen, six showed genetic disruptions with unknown consequences, and seven were predicted to lack this ability entirely. Variation within individuals was also found for bacteriocin classes and CRISPR-Cas genes.

CONCLUSIONS: Substantial functional diversity exists within L. crispatus, even among strains from the same individual, supporting the rationale for multi-strain vaginal probiotics. This citizen science approach enabled discovery of host-specific adaptations while ensuring participant ownership of their strains.},
}

@article {pmid42696079,
year = {2026},
author = {Mitra, S and Damini, and Devi, M and Niyogi, SG and Singh, UP and Lo, D and Bishtania, HC and Thakur, S},
title = {Unlocking the potential of bacteriophage-based therapeutic gene delivery in hepatocellular carcinoma.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {38},
number = {1},
pages = {},
pmid = {42696079},
issn = {2589-0409},
mesh = {Humans ; *Liver Neoplasms/therapy/genetics ; *Carcinoma, Hepatocellular/therapy/genetics ; *Bacteriophages/genetics ; *Genetic Therapy/methods ; *Gene Transfer Techniques ; Animals ; CRISPR-Cas Systems ; Genetic Vectors/genetics/administration & dosage ; Gene Therapy Agents ; },
abstract = {Liver cancer, mainly hepatocellular carcinoma (HCC), remains a global health burden marked by poor prognosis with limited therapeutic efficacy, and high recurrence rates. HCC remains one of the most lethal malignancies worldwide, with limited therapeutic options and high resistance to conventional treatments. Despite low therapeutic efficacy, molecular heterogeneity, treatment resistance and high recurrence rate, hepatocellular carcinoma (HCC) is still a significant health problem worldwide. These restrictions have stimulated the research of focused methods for delivering therapeutic genetic payload into cancer cells. Bacteriophages have been gaining growing attention as an emerging delivery platform due to their genetic versatility, ease of engineering, ability to be surface modified and payload targeted. In this narrative review, the therapeutic potential of engineered bacteriophages in the context of HCC therapy is critically analyzed focusing on phage display-mediated tumor targeting, phage-mediated intracellular gene delivery, TRAIL gene delivery, and CRISPR/Cas-based therapeutic strategies. It has been previously noted in the literature that phage display can be used to attach tumor-targeting ligands to the surface of a phage, which may aid in the recognition of receptors at the tumor site and promote targeted delivery to the receptor. Therapeutic application is stunted by inefficient trafficking to the cytosol, endosomal degradation, immune recognition and clearance, vector stability, manufacturing scalability and regulatory issues. In conclusion, engineered bacteriophages are a promising and versatile tool for targeted gene delivery in HCC but more mechanistic, preclinical and translational research is needed to prove their therapeutic effectiveness and clinical usefulness for this purpose.},
}

Humans
*Liver Neoplasms/therapy/genetics
*Carcinoma, Hepatocellular/therapy/genetics
*Bacteriophages/genetics
*Genetic Therapy/methods
*Gene Transfer Techniques
Animals
CRISPR-Cas Systems
Genetic Vectors/genetics/administration & dosage
Gene Therapy Agents