Abstract Pre-harvest sprouting (PHS), where seeds germinate on panicles before harvest under humid conditions, is a serious global issue in cereal crop production, including rice. OsERF94 was previously identified as a candidate gene associated with PHS through a genome-wide association study. In this study, we investigated the role of OsERF94 in PHS using CRISPR/Cas9 gene editing. The CRISPR/Cas9-mediated mutagenesis of OsERF94 induced frameshift mutations, resulting in a loss-of-function of OsERF94 in the 1-I-ET and 2-D-ET lines. The 1-I-ET and 2-D-ET lines exhibited significantly higher germination rates under PHS conditions compared to the wild type, indicating increased susceptibility to PHS. Whole-genome re-sequencing confirmed that few or no mutations could be detected at off-target candidate sites in both edited lines, ensuring the precision of the CRISPR/Cas9 gene editing. A transcriptome analysis revealed that OsERF94 modulates the expression of key GA biosynthetic and catabolic genes, including OsLOL1 , OsKO3 , OsGA3ox2 , and OsGA2ox5 , during both seed development and the early germination stages of PHS. The up-regulation of GA biosynthetic genes and the down-regulation of GA deactivation genes in both gene-edited lines likely led to elevated endogenous GA levels at 0 and 1 days after PHS, promoting germination under PHS conditions. These findings suggest that OsERF94 acts as a negative regulator of germination by modulating both GA biosynthesis and deactivation. Our findings contribute to expanding our knowledge of the molecular mechanisms of OsERF94 in PHS and highlight OsERF94 as a promising target for the genetic improvement of PHS resistance in rice-breeding programs.

Poison exons (PE) are highly conserved exon cassettes whose inclusion creates premature termination codons (PTCs) and triggers nonsense-mediated decay (NMD) of the mature transcript, therefore reducing protein expression. Despite their important role in post-transcriptional regulation, PEs remain poorly annotated due to the lack of systematic, transcriptome-wide approaches. In this study, we comprehensively investigated the function of PEs in the human brain and assessed the impact of pathogenic variants on their splicing. A comparative analysis of 957 eukaryotic transcriptomes revealed that humans exhibit the highest enrichment of NMD-targeted transcripts. To delineate the full landscape of PEs in the human transcriptome, we considered conserved (PhyloP score ≥ 20) alternatively spliced exons, less than 300 base pairs (bp) long, with the ability to introduce PTCs positioned more than 150 base pairs (bp) downstream of the transcription start site and outside the last two exons of the transcript. Our analysis identified 12,014 PEs in the human genome. For each PE, we calculated the percent-spliced-in (PSI) value across tissue types and developmental stages using GTEx and BrainSpan RNA-seq dataset, respectively. Overall, we identified 117 PEs uniquely found in the human brain, 1,214 PEs with brain-specific differential splicing compared to other tissues, and 1,610 PEs which splicing change during brain development. Integrating ClinVar and SpliceAI, we identified 1,877 annotated pathogenic variants predicted to affect the splicing of 891 PEs in the human brain. Notably, many of these variants were associated with neurodevelopmental and neurodegenerative disorders such as epilepsy, intellectual disability and frontotemporal dementia. We functionally validated the impact of selected variants using an optimized CRISPR prime-editing workflow in human cell lines. Our findings highlight PEs as pivotal regulators of gene expression in the human brain and establish a foundation for therapeutic strategies targeting PE mis-splicing in neurological diseases.

The two main cell types in the striatum, dopamine receptor 1 and adenosine receptor 2a spiny projection neurons (D1-SPNs and A2A-SPNs), have distinct roles in regulating motor- and reward-related behaviors. Cre-selective CRISPR-dCas9 systems allow for cell-type specific, epigenomic-based manipulation of gene expression with gene-specific single guide RNAs (sgRNAs) and have potential to elucidate molecular mechanisms underlying striatal subtype mediated behaviors. Conditional transgenic Rosa26:LSL-dCas9-p300 mice were recently generated to allow for robust expression of dCas9-p300 expression with Cre-driven cell-type specificity. This system utilizes p300, a histone acetyltransferase which regulates gene expression by unwinding chromatin and making that region of the genome more accessible for transcription. Rosa26-LSL-dCas9-p300 mice were paired with Drd1-Cre and Ador2a-Cre mice to generate Drd1-Cre:dCas9-p300 and Ador2a-Cre:dCas9-p300 mouse lines and underwent behavioral phenotyping when sgRNAs were not present. Both Drd1-Cre:dCas9-p300 and Ador2a-Cre:dCas9-p300 have cell-type specific expression of spCas9 mRNA. Baseline behavioral assessments revealed that, under a sgRNA absent nontargeted state, Drd1-Cre:dCas9-p300 mice display repetitive spinning behavior, hyperlocomotion and enhanced acquisition of reward learning in comparison to all genotypic littermates. In contrast, Ador2a-Cre:dCas9-p300 do not exhibit any changes in behavior in comparison to their littermates. Electrophysiological recordings of dorsal striatum D1-SPNs revealed that Drd1-Cre:dCas9-p300 mice have increased input resistance and increased spontaneous excitatory postsynaptic current amplitude, together suggesting greater excitatory drive of D1-SPNs. Overall, these data demonstrate the necessity to validate CRISPR-dCas9 lines for research investigations. Additionally, the Drd1-Cre:dCas9-p300 line has the potential to be used to study underlying mechanisms of stereotypy and reward-learning. Significance Statement Using CRISPR-based tools to identify cell-type specific epigenomic and transcriptional mechanisms in disease and behavior has high utility for the neuroscience field. Previous limitations related to implementation of CRISPR-editing systems in mice were thought to be overcome by the generation of transgenic mouse lines, including a novel Cre-dependent dCas9-p300 mouse line. Our data shows however that Drd1-Cre:dCas9-p300 mice, generated from breeding Drd1-Cre mice with the dCas9-p300 mice, have cellular and behavioral disruptions under a nontargeted sgRNA absent state. Overall, these data suggest caution in employing CRISPR-dCas9 systems, particularly transgenic mouse lines, for research investigations.

CRISPR-Cas genome editing toolkits have expanded the scope of genetic studies in various emerging model organisms. However, their applications are limited mainly to knockout experiments due to technical difficulties in establishing knock-in strains, which enables in vivo molecular tagging-based experiments. Here, we investigated knock-in strategies in the harlequin ladybug Harmonia axyridis, a model insect for evolutionary developmental biology, which shows more than 200 color pattern variations within a species. We tested several knock-in strategies using synthetic DNA templates. We found that ssDNA templates generated founder knock-in strains efficiently (2.5-11%), whereas the 5′ regions of ssDNA templates were frequently scraped when the insert length exceeded ~40 bases. To overcome this limitation, we designed several 3′ extended DNA templates. Of those, fast-annealed 3′-extended double-stranded DNA templates showed extremely high founder generation efficiency (32-67%) and accuracy (67-100%). This strategy is also applicable to the two-spotted cricket Gryllus bimaculatus, demonstrating that the fast-annealed 3′-extended dsDNA template is a highly potent and versatile DNA template for generating knock-in strains in emerging model insects for developmental genetic studies.

ABSTRACT The human malaria parasite Plasmodium falciparum ( Pf ) expresses ten thrombospondin type 1 repeat (TSR) domain-bearing proteins at different stages throughout its life cycle. TSRs can be modified by two types of glycosylation: O-fucosylation at conserved serine (S) or threonine (T) residues and C-mannosylation at conserved tryptophan (W) residues. Pf TRAP, which is expressed in mosquito-stage sporozoites, has one TSR domain that is O-fucosylated at Thr 256 and C-mannosylated at Trp 250 . We employed site-directed mutagenesis by CRISPR/Cas9 gene editing to generate two Pf TRAP glyco-null mutant parasites, Pf TRAP_T256A and Pf TRAP_W250F. The fitness of these mutant parasites across the life cycle was compared to the parental NF54 wild type as well as a Pf TRAP knockout line. The glyco-null parasites exhibited major fitness defects comparable to knockout: sporozoites were unable to productively colonize the salivary glands and were highly impaired in gliding motility and the ability to invade cultured human hepatocytes. Protein analysis revealed significantly reduced Pf TRAP abundance in the glyco-null mutants despite normal transcript levels. These findings demonstrate that glycosylation of Pf TRAP’s TSR is critical for its proper expression and function, and underscores the importance of TSR glycosylation in the mosquito stage of the life cycle.

Enterococcus faecalis is a gram-positive bacterium and a common cause of hospital-associated infections. Three major CRISPR loci have been discovered in this species, namely CRISPR1-cas, CRISPR2 and CRISPR3-cas. We developed novel primers which target the CRISPR1-cas loci in E. faecalis and tested these primers on 26 E. faecalis isolates isolated from diverse settings from Segamat, Malaysia. Half of the isolates were found to carry the CRISPR1-cas9 locus, and the CRISPR1 array was successfully amplified in 12 out of 13 isolates that contained the cas9 gene. Characterisation of the CRISPR array shows that CRISPR1-cas shares similar array length and typical repeat sequences with CRISPR2 but differ significantly in terms of spacer identities and terminal repeat (TR) sequences. Most CRISPR spacers encode for chromosomal DNA sequences. Genotype characterisation based on ancestral spacer (AS) and TR sequences indicate that E. faecalis with the same CRISPR1-AS genotype do not always harbour same CRISPR2-AS genotypes, and vice versa. A combined CRISPR1-cas and CRISPR2 typing offers comparable discriminatory power to multilocus sequence typing (MLST), suggesting its potential to be used in short-term strain identification and epidemiological surveillance at a lower sequencing cost. Our study provides a genetic reference for future studies in the Southeast Asia region.

Synthetic biology applied to baculoviruses enables genome optimization through the targeted deletion of nonessential genes, enhancing recombinant protein expression. In this study, the CRISPR/Cas9 system with two tandem sgRNAs was used and validated as an efficient strategy to remove independently large genomic fragments from AcMNPV, all encoding proteins dispensable for budded virus production. The resulting mutant viruses were evaluated for their ability to express eGFP and HRPc in Sf9 cells and in Rachiplusia nu and Spodoptera frugiperda larvae. Deletions of the Ac15–Ac16 and Ac129–Ac131 regions led to significant increases in protein expression in infected cells and in larvae. In contrast, deletion of the Ac136–Ac138 region enhanced expression only in cultured cells but had a negative impact on larvae. Removal of the Ac148–Ac150 fragment caused a marked reduction in expression in both experimental systems. These findings confirm that although some genes are nonessential for systemic infection, their combined deletion can differentially affect recombinant protein expression depending on the host. This study validates not only an effective strategy for developing minimized baculovirus genomes but also the use of dual-guide CRISPR/Cas9 editing as a rapid and precise tool for genome engineering in baculovirus-based expression systems.

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor α ( Esr1 ) was significantly increased by HFD, concomitant with a down-regulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 ( Dnmt1 ) and Dnmt3a, and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge; while mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in HFD-challenged mice. Our study demonstrates that DNA methylation at Esr1 promoter plays an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

ABSTRACT Phenotypic plasticity occurs when a genotype can produce more than one phenotype under different environmental conditions. Genetic accommodation allows plastic phenotypes to be tuned to new environments and eventually to even be lost via canalization/assimilation. The colourful and toxic Heliconiini butterflies have biochemical plasticity – they either sequester their cyanogenic glucosides (CG) from their larval hostplant or biosynthesize them when compounds for sequestration are not available. Here, we traced the evolution of CG biosynthesis in Heliconiini butterflies, a fundamental component of this biochemical plasticity. We first CRISPR-edited the CYP405s , which encode the first enzyme of this pathway in Heliconius erato, and confirmed that CYP405 -knockout caterpillars do not biosynthesize CGs. Then, we identified the CYP405 s and CYP332 s (the second gene in this pathway) in 63 species of the subfamily Heliconiinae, as well as in other lepidopterans. Most lepidopterans have a CYP332 , but CYP405 is mostly found in butterflies and has been duplicated in all Heliconius species. Both genes were independently co-opted into CG biosynthesis in the Heliconiinae butterflies and Zygaena moths, in which they were first functionally characterized. Finally, we performed ancestral reconstruction analyses of biochemical plasticity using data from over 700 Heliconiini butterflies. We demonstrated that although plasticity was ancestral in the whole tribe and allowed these butterflies to increase their hostplant range, it might have been lost in few specialized clades, such as the Sapho clade that just sequester CG from their hostplants. This clade has several CYP405 copies, but they lack structurally important P450 domains, which may explain why biosynthesized CGs are virtually lost in species of the Sapho clade. Our findings represent one of the few examples of plasticity-first evolution in which the genetic mechanisms associated with its accommodation/assimilation are known. This study also emphasizes the importance of co-option in the evolution of complex traits, such as toxicity.

Genome-wide association studies (GWAS) have identified numerous loci linked to late-onset Alzheimer’s disease (LOAD), but the pan-brain regional effects of these loci remain largely uncharacterized. To address this, we systematically analyzed all LOAD-associated regions reported by Bellenguez et al. using the FILER functional genomics catalog across 174 datasets, including enhancers, transcription factors, and quantitative trait loci. We identified 42 candidate causal variant-effector gene pairs and assessed their impact using enhancer-promoter interaction data, variant annotations, and brain cell-type-specific gene expression. Notably, the LOAD risk allele of rs74504435 at the SEC61G locus was computationally predicted to increase EGFR expression in LOAD related cell types: microglia, astrocytes, and neurons. Functional validation using promoter-focused Capture C, ATAC-seq, and CRISPR interference in the HMC3 human microglia cell line confirmed this regulatory relationship. Our findings reveal a microglial enhancer regulating EGFR in LOAD, suggesting EGFR inhibitors as a potential therapeutic avenue for the disease.

Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10 -/-embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1 . In situ hybridization studies showed that Rdh10 -/-embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a defect in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development. Highlights The RA requirement for optic cup formation was examined using Rdh10 knockout embryos. Eye RNA-seq and ChIP-seq (H3K27ac) identified Alx1 as a potential RA target gene. Alx1 exhibits RA-regulated H3K27ac deposition near exon 1 associated with a nearby RARE. Alx1 knockout embryos display a misfolded optic cup with a ventral defect similar to Rdh10 KO.

Cerebral small vessel disease is a leading cause of cognitive decline and stroke in the elderly, with cerebral microbleeds (CMBs) as one of the key imaging biomarkers. Our understanding of its pathophysiology remains limited due to the lack of appropriate animal models. We report a novel mouse CMB model created by disrupting collagen IV, a core component of the vascular basement membrane (BM), specifically within brain microvessels. Targeted deletion of Col4a1 was achieved in adult mice using brain endothelial-specific AAV vectors with CRISPR/Cas9. MRI revealed numerous CMBs with distributions similar to those of human CMBs. CMB burden increased progressively over six months following Col4a1 deletion in a dose-dependent manner, accompanied by cognitive decline and motor incoordination. Histological examination revealed hemosiderin deposits corresponding to MRI-detected CMBs without evidence of macroscopic hemorrhage or white matter lesions, while ultrastructural analysis demonstrated significant BM thinning in Col4a1 -depleted microvessels. Analysis of human MRI and genomic data identified significant associations between CMB susceptibility and genetic variants in TIMP2 , an endogenous inhibitor of the matrix-degrading enzyme MMP2, underscoring the clinical relevance of our model. These findings establish a direct causal relationship between microvessel COL4A1 and CMB, suggesting that dysregulated collagen IV homeostasis in BM underlies CMB development.

SUMMARY Despite the availability of RAS inhibitors and the dependence of >90% of pancreatic ductal adenocarcinomas (PDAC) on oncogenic KRAS mutations, resistance to KRAS inhibition remains a serious obstacle. We show here that phosphoinositide 3-kinase (PI3K) plays a major role in this resistance through upstream activation of wild-type RAS signaling – beyond its known KRAS effector function. Combining proximity labeling, CRISPR screens, live-cell imaging, and functional assays we found that PI3K orchestrates phosphoinositide-mediated GAB1 recruitment to the plasma membrane, nucleating assembly of RAS signaling complexes that activate mitogen-activated protein kinase (MAPK) in an EGFR/SHP2/SOS1-dependent manner. We further demonstrate that inhibiting PI3K enhances sensitivity to mutant-specific KRAS inhibitors in PDAC cells, including cells with clinically identified PIK3CA mutations. Our findings refine RAS-PI3K signaling paradigms, reveal that PI3K-driven wild-type RAS activation drives resistance to KRAS inhibition, and illuminate new avenues for augmenting KRAS-targeted therapies in PDAC.

SUMMARY Energy expenditure (EE) is essential for metabolic homeostasis, yet its central regulation remains poorly understood. Here, we identify arcuate Kiss1 neurons as key regulators of EE in male mice. Ablation of these neurons induced obesity, while their chemogenetic activation increased brown adipose tissue (BAT) thermogenesis without affecting food intake. This action is mediated by glutamatergic projections from Kiss1 ARC neurons to CART/Lepr-expressing neurons in the dorsomedial hypothalamus, which activate the raphe pallidus-BAT pathway. CRISPR-mediated deletion of the vesicular glutamate transporter 2 ( Vglut2) from Kiss1 ARC neurons replicated the obesogenic effect. Furthermore, deletion of the melanocortin 4 receptor (MC4R) from Kiss1 neurons resulted in obesity, reduced energy expenditure and impaired thermogenesis. Optogenetic stimulation of pro-opiomelanocortin (POMC) fibers evoked inward currents in Kiss1 neurons, that were attenuated by MC4R antagonism. Our findings reveal a previously unrecognized neural circuit that mediates melanocortin action on energy expenditure, offering new insights into central mechanisms of metabolic control.

Abstract Active transport of chemical species across the cell membrane represents a critical biological and biotechnological function, allowing the cell to selectively import compounds of nutritional value whilst exporting potentially toxic compounds. Major facilitator superfamily (MFS) transporters represent a ubiquitous class able to uptake and export an array of different chemical species. When designing biosynthetic pathways within microbial hosts, for production or remediation, transport is often critical to the efficiency of the resulting engineered strain. However, transport is a commonly neglected node for characterisation and engineering given difficulties in producing, purifying and assaying membrane transport proteins outside of their native environment. Here, using syntenic analysis and genetically encoded biosensors a library of MFS transporters were screened for their ability to uptake the aromatic acids, protocatechuic acid and terephthalic acid. The structure activity relationships of the corresponding transporters, PcaK and TphK, were then assessed with library of aromatic acid effectors. Finally, the feasibility of protein engineering was assessed, by the creation of chimeric MFS transporters, revealing a degree of effector recognition plasticity and the modularity of core transmembrane domains. This study provides a library of validated MFS transporters and demonstrates the value of employing genetically encoded biosensors in the characterisation and engineering of this important transport function.

Huntington’s disease (HD) is a monogenic autosomal dominant neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene, yielding a gain-of-toxic-function mutant Huntingtin protein mHTT. CRISPR/Cas9 is a potentially powerful therapeutic tool for treating HD by eliminating mutant HTT (m HTT ) gene. We developed a specific SaCas9 guide RNA to target human m HTT , and a self-inactivating gene editing system that abolishes SaCas9 after a short transient expression for high gene editing efficiency and maximal safety to prevent off-target effects. Both conventional and the new self-inactivating gene editing systems achieved successful elimination of m HTT gene, 60-90% mHTT protein and 90% of mHTT aggregation in BAC226Q HD mouse brains, which resulted in significant long-term rescue of neural pathology, motor deficits, weight loss and shortened lifespan. These beneficial effects were observed when gene editing was applied before, at and well after the on-set of pathological and behavioral abnormalities. These proof-of-concept data demonstrate that gene editing can be a highly effective therapeutic approach for HD and other inherited neurodegenerative diseases. One Sentence Summary Self-inactivating CRISPR for mutant huntingtin in HD mice achieved long-term rescue of neural pathology, motor deficits, weight loss and survival.

The advent of CRISPR/Cas systems has revolutionized plant genome engineering, transitioning from traditional single-gene edits to sophisticated multiplex genome editing strategies capable of simultaneously targeting multiple loci. This review provides an in-depth examination of CRISPR-mediated multiplexing technologies in plants, emphasizing their molecular mechanisms, delivery systems, and transformative applications in crop improvement. We delineate the evolution of CRISPR systems from early programmable nucleases to diverse Class 2 effectors, including Cas9, Cas12, Cas13, and emerging ultra-compact variants like CasΦ and Cas14. We detail polycistronic gRNA expression platforms—such as tRNA-sgRNA arrays, ribozymes, and Csy4-mediated cleavage—that enable efficient multi-target editing within compact vectors. Furthermore, we explore advanced delivery modalities including Agrobacterium, biolistics, protoplast transfection, and viral vectors, optimized for recalcitrant plant systems. Applications span yield enhancement, disease resistance, abiotic stress tolerance, nutritional fortification, and de novo domestication. Critical challenges including off-target mutagenesis, mosaicism, chromosomal rearrangements, and regulatory constraints are addressed. Finally, we highlight AI-driven sgRNA design, multi-omics integration, and CRISPR libraries as pivotal tools to rationalize and scale multiplex editing. This synthesis underscores multiplex CRISPR as a cornerstone of next-generation plant breeding, with the potential to redefine global agriculture through precision trait stacking and rapid varietal development.

Bacteriophages (phages), the most abundant biological entities on Earth, have long served as both model systems and therapeutic tools. Recent advances in synthetic biology and genetic engineering have revolutionized the capacity to tailor phages with enhanced functionality beyond their natural capabilities. This review outlines the current landscape of synthetic and functional engineering of phages, encompassing both in vivo and in vitro strategies. We describe in vivo approaches such as phage recombineering systems, CRISPR-Cas-assisted editing, and bacterial retron-based methods, as well as synthetic assembly platforms including yeast-based artificial chromosomes, Gibson, Golden Gate, and iPac assemblies. In addition, we explore in vitro rebooting using TXTL (transcription-translation) systems, which offer a flexible alternative to cell-based rebooting but are less effective for large genomes or structurally complex phages. Special focus is given to the design of customized phages for targeted applications, including host range expansion via receptor-binding protein modifications, delivery of antimicrobial proteins or CRISPR payloads, and the construction of bio-contained, non-replicative capsid systems for safe clinical use. Through illustrative examples, we highlight how these technologies enable the transformation of phages into programmable bactericidal agents, precision diagnostics tools, and drug delivery vehicles. Together, these advances establish a powerful foundation for next-generation antimicrobial platforms and synthetic microbiology.

SNX11, a sorting nexin protein localized on the endosomal membrane, is an important protein closely related to protein sorting and endosomal trafficking. Previously, through a genome-wide CRISPR screening, we identified SNX11 as a critical protein for the entry of Dabie bandavirus. SNX11-deletion significantly inhibits the replication of Dabie bandavirus. We further discovered that the loss of SNX11 alters endosomal pH, potentially affecting the release process of Dabie bandavirus from endosomes to the cytoplasm. However, the mechanism by which SNX11 modulates endosomal pH and whether SNX11-deletion similarly inhibits other viruses remain to be elucidated. This study reveals that SNX11 can interact with the V1 subunit of the endosomal proton pump V-ATPase, affecting the expression level of this subunit on the endosomal membrane and thereby disrupting the assembly of V-ATPase. Additionally, we found that SNX11-deletion significantly inhibits the replication of dengue virus, hantavirus, and influenza virus. These findings suggest that SNX11 may be a key protein in the process of viral infection and could serve as a broad-spectrum antiviral target.

Glioblastoma (GBM) is a lethal brain tumor with limited response to standard of care chemoradiotherapy. In this study, we conducted genome-wide CRISPR knockout screening in patient-derived glioblastoma stem cells (GSCs) to identify genetic dependencies of cell survival and therapy resistance. Our screening identified flap endonuclease 1 (FEN1) as a key driver of GSC survival, with enhanced dependency under temozolomide (TMZ) treatment. Genetic perturbation of FEN1 reduced GSC self-renewal and proliferation in vitro, and prolonged survival in a patient-derived xenograft model of GBM. FEN1 inhibition (FEN1i) preferentially affected highly aggressive or recurrent GBM models compared with less aggressive GBMs and healthy neural stem cells. Moreover, FEN1 inhibition synergized with TMZ only in these aggressive FEN1i-sensitive GSCs, providing cancer-selective killing and TMZ sensitization in the most untreatable of GBMs. Mechanistically, FEN1i-sensitive GSCs exhibited greater proliferation and sphere formation, while stalling their proliferation conferred resistance to FEN1 inhibition. Single-cell transcriptomics further linked FEN1 expression to stemness and the DNA damage response, elucidating broader determinants of FEN1 dependency. These findings establish FEN1 as a promising therapeutic target in GBM, offering a strategy for both selective targeting and enhancement of TMZ efficacy in aggressive cancers. Statement of Significance This study identifies FEN1 as a key vulnerability of glioblastoma stem cells, revealing its role in therapy resistance and stemness, and proposes FEN1 inhibition as a strategy to enhance temozolomide efficacy.

RNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted RNA-seq or targeted amplicon-seq, involve high costs, complex workflows, and limited accessibility. To address these limitations, we developed a rapid and cost-effective long-read sequencing approach, termed premium PCR sequencing, for digital quantification of RNA-editing and intron retention events in targeted chloroplast transcripts. This method combines multiplexed high-fidelity PCR amplification with Oxford Nanopore sequencing and custom in-house Perl and Python scripts for streamlined data processing, including barcode-based demultiplexing, strand reorientation, alignment to a pseudo-genome, manual editing-site inspection, and splicing variant identification and comparison. Using this platform, we analyzed the ndhB and ndhD transcripts, two chloroplast NAD(P)H dehydrogenase genes with the highest number of known editing sites, in an inducible CRISPR interference (iCRISPRi) system targeting MORF2 , a key RNA-editing factor. Our results revealed MORF2 dosage-dependent reductions in C-to-U editing efficiency, with significant defects observed in the strongly repressed P1-12 line. Moreover, we identified an accumulation of intron-retaining ndhB transcripts, specifically in Dex-treated iCRISPRi lines, indicating impaired chloroplast splicing functions upon MORF2 suppression. The platform achieves single-molecule resolution, robust reproducibility, and high read coverage across biological replicates at a fraction of the cost of lncRNA-seq, making it broadly accessible. This study establishes premium PCR sequencing as a versatile, scalable, and affordable tool for targeted post-transcriptional analysis in plant organelles and expands our understanding of MORF2’s role in chloroplast RNA maturation. Significance Statement We present a rapid, affordable, and reproducible method for digital quantification of RNA editing and intron retention in plant organellar transcripts using nanopore-based long-read sequencing. This platform overcomes key limitations of existing approaches and enables routine, site-specific analysis of post-transcriptional regulation in organelles, including RNA editing and splicing, making it broadly accessible to researchers studying plastid biology, stress responses, and organelle–nucleus communication.

ABSTRACT Background Fibrillins are essential components of the extracellular matrix. Marfan syndrome (MFS), the most common fibrillinopathy, is characterized by severe cardiovascular complications, including cardiac valve abnormalities, myocardial dysfunction, arrhythmias, and, most commonly, thoracic aortic disease. Unfortunately, no definitive medical cure is available. Objectives To establish a zebrafish model of MFS, to enhance understanding of the cardiovascular consequences of fibrillin impairment and identify novel therapeutic targets. Methods CRISPR/Cas9 technology was used to systematically target all zebrafish fibrillin genes. The cardiovascular phenotype was investigated using fluorescent microscopy at embryonic stages and cardiac ultrasound, histology, and synchrotron X-ray imaging in adults. RNA sequencing and drug testing were performed during early development. Results Fibrillin-2b mutant ( fbn2b -/- ) zebrafish had a reproducible phenotype, with a subset of embryos showing endocardial detachment leading to early mortality. Interestingly, the remaining fbn2b -/- zebrafish developed dilation of the bulbus arteriosus, a structure analogous to the aortic root in humans, and survived normally to adulthood. Adult fbn2b -/- zebrafish displayed cardiac valve abnormalities. Transcriptomic analysis of fbn2b -/- embryos suggested the involvement of extracellular matrix remodeling and immune-related pathways. Administration of nebivolol and losartan did not improve the phenotype of fbn2b -/- larvae. Zebrafish lacking fibrillin-1 and/or fibrillin-2a did not show any phenotype. Conclusion Our fbn2b -/- zebrafish model recapitulates key aspects of human cardiovascular manifestations of MFS and can therefore be considered a novel relevant animal model for MFS. Studying this model allows us to broaden the knowledge of the underlying mechanisms of the disease and discover much-needed disease-specific treatment options. CONDENSED ABSTRACT Fibrillin defects lead to severe cardiovascular complications in Marfan syndrome (MFS), including aortic dilation, dissection, and rupture. To model MFS, we generated zebrafish mutants lacking various fibrillin genes. Among these mutant lines, only fibrillin-2b-deficient zebrafish exhibited cardiovascular phenotypes mimicking human disease. Multimodal imaging revealed early cardiac defects, bulbus arteriosus dilation, and valve abnormalities. Transcriptomic analysis identified altered regulation of pathways related to extracellular matrix homeostasis and immune system activation. Compound testing demonstrated the model’s potential for drug discovery. This zebrafish model, recapitulating key cardiovascular features of MFS, provides a valuable platform to investigate disease mechanisms and identify novel treatment strategies.

Abstract γδ T cells are mediators of immunosurveillance used in the clinic. However, their status remains paradoxical. While many display overt traits of adaptive immunity, several major γδ cell subsets including those in barrier tissues make rapid, seemingly TCR-independent responses phenocopying innate lymphoid cells (ILC). While such uncertainty exists, the requirements for γδ T cell-mediated immunosurveillance will remain unclear. This study resolves the paradox, showing that tissue-intrinsic γδ T cells share an absolute real-time dependence on the TCR for their phenotypes, including so-called innate responses to tissue stress and carcinogenesis. While different tissue-intrinsic γδ subsets showed distinct TCR-dependencies, we identified a shared set of TCR-regulated molecules that was likewise disrupted by acute TCR ablation in human γδ T cells. These findings unequivocally distinguish γδ cells from ILC and establish that immunosurveillance by γδ T cells requires an environment conducive to TCR signalling.[139]

ABSTRACT The recent global outbreaks of mpox highlight the urgent need for both fundamental research and antiviral development. However, studying monkeypox virus (MPXV), with its large and complex genome, remains challenging due to the requirement for high-containment facilities. Here, we describe a novel strategy for de novo assembly of MPXV clade IIb genomes in bacterial artificial chromosomes using transformation-associated recombination cloning. Leveraging CRISPR-Cas9 and Lambda Red recombination, we engineered replication-defective MPXV particles with dual deletions of OPG96 ( M2R ) and OPG158 ( A32.5L )—genes essential for virion assembly, that are capable of recapitulating key stages of the viral life cycle. Our work demonstrates the utility of replication-defective MPXV particles as a reliable platform for high-throughput antiviral discovery, offering significant advantages for both fundamental virology studies and therapeutic development against orthopoxviruses.

ABSTRACT Post-transcriptional modifications expand the information encoded by an mRNA. These dynamic and reversible modifications are specifically recognized by reader RNA-binding proteins (RBPs), which mediate the regulation of gene expression, RNA processing, localization, stability, and translation. Given their crucial functions, any disruptions in the normal activity of these readers can have significant implications for cellular health. Consequently, the dysregulation of these RBPs has been associated with neurodegenerative disorders, cancers, and viral infections. Therefore, there has been growing interest in targeting reader RBPs as a potential therapeutic strategy since developing molecules that restore proper RNA processing and function may offer a promising avenue for treating diseases. In this work, we coupled our previously established live-cell RNA-protein interaction (RPI) assay, RNA interaction with Protein-mediated Complementation Assay (RiPCA), with CRISPR technology to build a new platform, CRISPR RiPCA. As a model for development, we utilized the interaction of eukaryotic translation initiation factor 4E (eIF4E), a reader RBP that binds to the m 7 GpppX cap present at the 5′ terminus of coding mRNAs, with an m 7 G capped RNA substrate. Using eIF4E CRISPR RiPCA, we demonstrate our technology’s potential for measuring on-target activity of inhibitors of the eIF4E RPI of relevance to cancer drug discovery.