Abstract Directional cell migration plays a central role in a wide range of physiological and pathological conditions, such as embryonic development or tumor metastasis. Steps involved in cell migration include cell polarization, formation of membrane protrusions at the cell front side and adhesion disassembly at the rear side, and a general cytoskeletal rearrangement. Overall it is a complex phenomenon at the interface between mechanical forces and biochemical signaling, with cell-specific and context-specific molecular events acting in the process. Here, we focus on human fibroblast migration induced by a biochemical gradient with an approach that connects the identification of molecular players with the actual mechanical function. We show how to screen for genes and miRNAs involved in migration by the direct integration of a high-throughput gene editing method, the CRISPR-Cas9 knockout pool screening, and a well-established functional assay, the transwell migration assay. Moreover, the screening has been performed after an expansion step aiming at the removal of all the essential genes and miRNAs, so to identify targets related to the cell migratory ability without affecting other major cellular functions. The results confirm known genes involved in migration, but also highlight new candidates. This work establishes a methodological advancement in the use of CRISPR technology for functional screening, and represents a resource for candidate genes and miRNAs playing a role in human fibroblast directional migration under biochemical gradient.

Background: Genomic variations contribute to the phenotypic diversity of individuals. A number of polymorphisms in protein-coding regions that alter drug efficacy or lead to adverse reactions have been characterized; however, noncoding regions that affect drug responses are largely overlooked, except for a limited number of well-studied enhancers. Results We conducted a quantitative assessment of cis-regulatory elements (CREs) based on transcription initiation profiling of mRNAs and noncoding RNAs, including enhancer RNAs, by using CAGE (Cap Analysis of Gene Expression). Candidate CREs identified in a hepatocellular carcinoma HepG2 cell line with stable expression of drug-responsive transcription factor pregnane X receptor (PXR) were further narrowed down by integrating data of PXR-binding sites in human primary hepatocytes and genome-wide association studies. We found more than 100-fold enrichments of the candidates to genetically associated loci with circulating levels of bilirubin and vitamin D, which implicated a link to adverse reactions of PXR ligands. We uncovered novel enhancers of UGT1A1 and TSKU through CRISPR/Cas9 knockout experiments. We identified alleles altering regulatory activities of UGT1A1 and CYP24A1enhancers by using luciferase reporter assay. Furthermore, our siRNA experiments revealed an unexpected impact of TSKU on the expression of vitamin D-metabolizing enzymes. Conclusions Our transcriptome-based assessment of CREs expanded the list of drug-inducible and PXR-mediated enhancers and super-enhancers. We identified regulatory alleles that alter drug-induced gene expressions, and discovered a novel molecular cascade associated with an adverse reaction. Our results contribute a precise understanding of the noncoding elements of the human genome underlying drug responses.

Background: Mitral Valve Prolapse (MVP) is a prevalent valvular disorder linked to considerable morbidity and mortality, affecting approximately 2.4% of the general population. A prior genome association study linked LTBP2 to this trait. We report a knockout mouse with LTBP2 mutation demonstrating valve phenotype as well as a family with a novel mutation causing MVP Methods: Exome sequencing and segregation analysis were conducted on a large pedigree to identify mutations associated with MVP. Using CRISPR-Cas9 technology, two strains of mice were generated: one with a complete knockout (KO) of the LTBP2 gene and another with a knock-in (KI) mutation corresponding to the putative causative mutation. Echocardiography and histological examinations of valves were performed in the KO and the KI at the age of 6 months. Optical coherence tomography (OCT) and histological examination of the eyes was done at the same time. mRNA qPCR analysis for TGFβ signaling targets (periostin/POSTN, RUNX2, and CTGF) in valve tissues was analyzed. Results: The LTBP2 rs117800773 V1506M mutation exhibited segregation with the MVP trait. LTBP2 KO mice had higher incidence of myxomatous changes by histology (7 of 9 of KO vs. 0 of 7 control animals, p=0.00186) and echocardiography (7 of 9 vs. 0 of 8, p=0.0011). LTBP2 Knock-in mice for the human mutation showed a significantly elevated myxomatous histological phenotype (8 of 8 vs. 0 of 9, p=0.00004) as well as by echocardiography (6 of 8 vs. 0 of 9, p=0.00123). KO mice demonstrated a significant increase in the depth of the anterior chamber as well as reduced visual acuity. LTBP2 KO mice demonstrated overexpression of both TGFβ signaling targets RUNX2 and periostin (P=0.0144 and P=0.001826, respectively). Conclusion: Animal models of LTBP2 KO and KI recapitulate MVP phenotype indicating that LTBP2 mutations are indeed causing myxomatous degeneration. Further, LTBP2 rs117800773 V1506M segregated with MVP in a large pedigree. Our data indicate the importance of LTBP2 in normal mitral valve function and that mutations in the gene care causing myxomatous valve.

Objective: Genome wide association studies have identified an exon 6 CTRB2 deletion variant that associates with increased risk of pancreatic cancer. To acquire evidence on its causal role, we developed a new mouse strain carrying an equivalent variant in Ctrb1, the mouse orthologue of CTRB2. Design: We used CRISPR/Cas9 to introduce a 707bp deletion in Ctrb1 encompassing exon 6 (Ctrb1-delexon6). This mutation closely mimics the human deletion variant. Mice carrying the mutant allele were extensively profiled at 3 months to assess their phenotype. Results: Ctrb1-delexon6 mutant mice express a truncated CTRB1 that accumulates in the ER. The pancreas of homozygous mutant mice displays reduced chymotrypsin activity and total protein synthesis. The histological aspect of the pancreas is inconspicuous but ultrastructural analysis shows evidence of dramatic ER stress and cytoplasmic and nuclear inclusions. Transcriptomic analyses of the pancreas of mutant mice reveals acinar program down-regulation and increased activity of ER stress-related and inflammatory pathways. Heterozygous mice have an intermediate phenotype. Agr2 is one of the most up-regulated genes in mutant pancreata. Ctrb1-delexon6 mice exhibit impaired recovery from acute caerulein-induced pancreatitis. Administration of TUDCA or sulindac partially alleviates the phenotype. A transcriptomic signature derived from the mutant pancreata is significantly enriched in normal human pancreas of CTRB2 exon 6 deletion variant carriers from the GTEx cohort. Conclusions: This mouse strain provides formal evidence that the Ctrb1-delexon6 variant causes ER stress and inflammation in vivo, providing an excellent model to understand its contribution to pancreatic ductal adenocarcinoma development and to identify preventive strategies.

Directed evolution is an efficient strategy to steer protein function to either understand specific biological properties or develop new biotechnology tools. Currently available methods for targeted mutagenesis in human cells rely on deaminases which can only modify specific bases, limiting the region of sequence space explored during evolution. By leveraging CRISPR-Cas9 coupled with an error-prone variant of human DNA polymerase λ, here we developed CRISPR-λ, an unbiased mutagenesis tool for directed evolution in human cells. We evaluated CRISPR-λ by reverting the fluorescence of a mutated EGFP and characterized it using ultra-deep sequencing. The mutagenic activity of CRISPR-λ spans 36-46 nucleotides from the target site, with a mutation frequency as high as 1.4e-4 substitutions per base and with no bias for specific nucleotide substitutions. The versatility of CRISPR-λ extends beyond base substitution, enabling modifications of the target gene through insertions and deletions, thereby broadening its potential for genetic diversification. We validated the efficacy of CRISPR-λ in directed evolution approaches by functionally reverting a mutated blasticidin resistance gene. Furthermore, we demonstrated the sequence diversification power of CRISPR-λ by steering the syncytia formation activity of the SARS-CoV-2 Spike envelope protein in cultured cells.

Recent discoveries have shown the presence of RNA molecules on the cell surface, defying the traditional view that RNA only functions intracellularly. However, it is not well understood how cell-surface RNA (csRNA) is stably present on the plasma membrane and what functions it performs on the cell surface. By exploiting the RNA-sensing ability of TLR7 as a specific recombinant probe to detect csRNA and coupling it with a genome-wide CRISPR-Cas9-knockout screening to identify genes essential for csRNA presentation on cells, we identified heparan sulfate (HS) as a crucial factor for RNA presentation on cells. Using the TLR7 binding probe, cell surface proximity labelling revealed that csRNA associates mechanistically with a plethora of RNA-binding proteins, and these interactions are crucial for csRNA presentation. Moreover, csRNA modulates receptor-ligand interactions between poliovirus receptor (PVR) and killer cell immunoglobulin-like receptor 2DL5 (KIR2DL5) by acting as a co-binder, recruiting the latter to cell surface. We provide a mechanistic understanding of csRNA presentation and unveil a new layer of complexity in the csRNA-dictated regulation of cell surface receptor-ligand interactions.

The widespread application of genome editing to treat or even cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped Delivery Vehicles (EDVs) are engineered virally-derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication components in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs, and demonstrated increased editing in cell lines and therapeutically-relevant primary human T cells. These results show that virally-derived particles can be streamlined to create efficacious genome editing delivery vehicles that could simplify production and manufacturing.

Melanoma being one of the most common and deadliest skin cancers, has been rising since the past decade. Patients at advanced stages of the disease have very poor prognoses, as opposed to at the earlier stages. Nowadays the standard-of-care of advanced melanoma is resection followed by immune checkpoint inhibition based immunotherapy. However, a substantial proportion of patients either do not respond or develop resistances. This underscores a need for novel approaches and therapeutic targets as well as a better understanding of the mechanisms of melanoma pathogenesis. Long non-coding RNAs (lncRNAs) comprise a poorly characterized class of functional players and promising targets in promoting malignancy. Certain lncRNAs have been identified to play integral roles in melanoma progression and drug resistances, however systematic screens to uncover novel functional lncRNAs are scarce. Here, we profile differentially expressed lncRNAs in patient derived short-term metastatic cultures and BRAF- MEK-inhibition resistant cells. We conduct a focused growth-related CRISPR-inhibition screen of overexpressed lncRNAs, validate and functionally characterize lncRNA hits with respect to cellular growth, invasive capacities and apoptosis in vitro as well as the transcriptomic impact of our lead candidate the novel lncRNA XLOC_030781. In sum, we extend the current knowledge of ncRNAs and their potential relevance on melanoma.

Mycobacterium tuberculosis ( Mtb ) infection of macrophages reprograms cellular metabolism to promote lipid retention. While it is clearly known that intracellular Mtb utilize host derived fatty acids and cholesterol to fuel the majority of its metabolic demands, the role of macrophage lipid catabolism on the bacteria’s ability to access the intracellular lipid pool remains undefined. We utilized a CRISPR genetic knockdown approach to assess the impact of sequential steps in fatty acid metabolism on the growth of intracellular Mtb . Our analyzes demonstrate that knockdown of lipid import, sequestration and metabolism genes collectively impair the intracellular growth of Mtb in macrophages. We further demonstrate that modulating fatty acid homeostasis in macrophages impairs Mtb replication through diverse pathways like enhancing production of pro-inflammatory cytokines, autophagy, restricting the bacteria access to nutrients and increasing oxidative stress. We also show that impaired macrophage lipid droplet biogenesis is restrictive to intracellular Mtb replication, but increased induction of the same by blockade of downstream fatty acid oxidation fails to rescue Mtb growth. Our work expands our understanding of how host fatty acid homeostasis impacts Mtb growth in the macrophage. Significance Mycobacterium tuberculosis ( Mtb ) primarily infects macrophages in the lungs. In infected macrophages, Mtb uses host lipids as key carbon sources to maintain infection and survive. In this work, we used a CRISPR-Cas9 gene knockout system in murine macrophages to examine the role of host fatty acid metabolism on the intracellular growth of Mtb . Our work shows that macrophages which cannot either import, store or catabolize fatty acids restrict Mtb growth by both common and divergent anti-microbial mechanisms, including increased glycolysis, increased production of reactive oxygen species, production of pro-inflammatory cytokines, enhanced autophagy and nutrient limitation. Our findings demonstrate that manipulating lipid metabolism in macrophages controls Mtb through multiple other mechanisms, beyond limiting the bacteria’s access to nutrients.

G protein-coupled receptors (GPCRs) are the largest class of membrane-bound receptors and transmit critical signals from the extracellular to the intracellular spaces. Transcriptomic data of resected breast tumors shows that low mRNA expression of the orphan GPCR GPR52 correlates with reduced overall survival in breast cancer patients, leading to the hypothesis that loss of GPR52 supports breast cancer progression. CRISPR-Cas9 was used to knockout GPR52 in human triple-negative breast cancer (TNBC) cell lines MDA-MB-468 and MDA-MB-231, and in the non-cancerous breast epithelial cell line, MCF10A. Loss of GPR52 was found to be associated with increased cell-cell interaction in 2D cultures, altered 3D morphology and increased propensity to organize and invade collectively in Matrigel. Furthermore, GPR52 loss was associated with features of EMT in MDA-MB-468 cells. To determine the in vivo impact of GPR52 loss, MDA-MB-468 cells were injected into zebrafish and loss of GPR52 was associated with a greater total cancer area compared to control cells. RNA-sequencing and proteomic analyses of GPR52-null breast cancer cells revealed an increased cAMP signaling signature. Consistently, we found that treatment of wild-type (WT) cells with forskolin, which stimulates production of cAMP, induces some phenotypic changes associated with GPR52 loss, and inhibition of cAMP production rescued some of the GPR52 KO phenotypes. Overall, our results reveal GPR52 loss as a potential mechanism by which breast cancer progression may occur and support the investigation of GPR52 agonism as a therapeutic option in breast cancer.

Abstract Targeted genome editing in pigs for optimizing pig productivity, disease tolerance and biomedical research has been widely undertaken by researchers. The present study aims to investigate the research advancements, focus area, gaps and challenges in the field of genome editing in pigs using bibliometric analysis. Bibliographic information of publications on genome editing in pigs from 2010 to 2023 were retrieved from Scopus database. Bibliometric analysis for parameters and network visualization like co-authorship, keyword co-occurrence, citation, bibliographic coupling and co-citation was conducted using VOSviewer. Literature mining was conducted to evaluate the emerging areas and challenges in the development of gene edited pigs. We found 727 documents on genome editing in pigs, of which 407 were research articles, authored by 2826 researchers from 1359 research organizations across 40 countries. The two countries China and United States, account for more than 50% of the research publications. Investigations on optimization of procedure, delivery methods, editing efficiency, reducing off-target dominated the early phase of research, which shifted to its application for generating knock out (KO) or knock in (KI) pigs in the recent years. Areas like xenotransplantation, disease resistance, higher muscling and disease model have dominated the research horizon. Emerging areas include base editing, CRISPR based screens, diagnostics and therapeutics. Investigations on reducing heat stress and environmental footprints through genetic alterations need more attention of scientists. The challenges like off-target effect, regulatory, ethical and societal issues for channelizing gene edited pigs from lab-to-land and then from farm-to-fork continue to restrain this field.

Abstract Background Pseudomonas putida KT2440, a non-pathogenic soil bacterium, is a key platform strain in synthetic biology and industrial applications due to its robustness and metabolic versatility. Various systems have been developed for genome editing in P. putida , including transposon modules, integrative plasmids, recombineering systems, and CRISPR/Cas systems. However, rapid iterative genome editing is limited by the complex and lengthy processes. Results We discovered that the pBBR1MCS2 plasmid carrying the CRISPR/Cas9 module could be easily cured in P. putida KT2440 at 30 o C. We then developed an all-in-one CRISPR/Cas9 system for yqhD and ech-vdh-fcs deletions, respectively, and further optimized the editing efficiency by varying homology arm lengths and target sites. Sequential gene deletions of vdh and vanAB was carried out rapidly using single-round processing and easy plasmid curing. This system's user-friendliness was validated by novice users in two labs for various gene deletions, substitutions, and insertion. Finally, iterative genome editing was used to engineering P. putida for valencene biosynthesis, achieving a 10-fold increase in yield. Conclusions We developed and applied a rapid all-in-one plasmid CRISPR/Cas9 system for genome editing in P. putida . This system requires lest than 1.5 days for one edit due to simplified plasmid construction, electroporation and curing processes, thus accelerating the cycle of genome editing. To our knowledge, this is the fastest iterative genome editing system for P. putida . Using this system, we rapidly engineered P. putida for valencene biosynthesis for the first time, showcasing the system's potential for expanding biotechnological applications.

ABSTRACT ATR (Ataxia Telangiectasia and Rad3-related) kinase and its interacting protein ATRIP orchestrate the replication stress response. Two patients of independent ancestry with microcephaly, primordial dwarfism, and recurring infections were found to be homozygous for splice donor site variants of ATRIP exon 5, resulting in ATRIP deficiency. The c.829+5G>T patient exhibited autoimmune hemolytic anemia, lymphopenia, poor vaccine response, and intermittent neutropenia. Immunophenotyping revealed reduced CD16 + NK cells and absent naïve T cells, mucosal-associated invariant T cells (MAITs), and invariant natural killer T cells (iNKTs). Lymphocytic defects were characterized by T cell receptor (TCR) oligoclonality, abnormal class switch recombination (CSR), and impaired T cell proliferation. ATRIP deficiency resulted in low-grade ATR activation but impaired CHK1 phosphorylation upon genotoxic stress. Consequently, ATRIP deficient cells inadequately regulated DNA replication, leading to chromosomal instability, compromised cell cycle control, and impaired cell viability. CRISPR-Select TIME confirmed reduced cell fitness induced by both variants. This study establishes ATRIP deficiency as a monogenic cause of microcephalic primordial dwarfism, highlights ATRIP’s critical role in protecting immune cells from replication stress, and brings a renewed perspective to the canonical functions of ATRIP.

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant re-sponses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial reg-ulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly en-hancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

Disruptions in circadian rhythm, partly controlled by the hormone melatonin, increase the risk of type 2 diabetes (T2D). Accordingly, a variant of the gene encoding the melatonin receptor 1B ( MTNR1B ) is robustly associated with increased risk of T2D. This single nucleotide polymorphism (SNP; rs10830963; G-allele) is an expression quantitative trait locus (eQTL) in human pancreatic islets, conferring increased expression of MTNR1B , which is thought to perturb pancreatic β-cell function. To understand this pathogenic mechanism in detail, we utilized human induced pluripotent stem cells (hiPSC), derived from individuals with T2D carrying the MTNR1B G-allele. Patient-derived fibroblasts were reprogrammed to hiPSC and single-base genome editing by CRISPR/Cas9 was employed to create isogenic lines of either the C/C or G/G genotypes (non-risk and risk, respectively). In addition, the human embryonic stem cell (hESC) line (HUES4) was subjected to genome editing to create isogenic lines of either the C/C or G/G genotypes. hiPSC and hESC were differentiated into β-cells, using a 50-day 2D protocol. Single-base genome editing generated cells with the desired genotype at a success rate of >90%. Expression of stage-specific markers confirmed differentiation of both hiPSC and hESC into β-cells. MTNR1B mRNA levels were consistently low in differentiated β-cells, precluding quantitative analysis of gene expression. However, Western blot analysis showed higher levels of MTNR1B in differentiated β-cells carrying the risk allele, consistent with rs10830963 (G-allele) being an eQTL in β-cells. Insulin secretion in response to glucose and IBMX was similar between the genotypes, whereas addition of melatonin reduced secretion in G-allele carriers. We conclude that the stem cell-derived β-cells are not sufficiently mature to allow determination of eQTL status at the mRNA level. However, we did observe increased MTNR1B protein and increased sensitivity of β-cells from risk allele carriers (G-allele) to melatonin with regard to insulin secretion, thus supporting a functional role for the rs10830963 SNP in β-cell dysfunction.

Abstract Calcium signals regulate crucial cellular functions yet many genes coding for Ca 2+ handling proteins remain unknown as their identification relies on low-throughput single-cell approaches. Here we describe a novel method to measure Ca 2+ activity in cells isolated by flow cytometry following pooled genome interrogation. Using a CRISPR/ CAMPARI2 screen, we identified enhancers and inhibitors of homeostatic Ca 2+ activity.

Type I-E CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) system is the most widely investigated RNA-guided adaptive immune system in prokaryotes against the foreign genetic elements. Unlike the previously characterized Cas3 nuclease in the typical Type I-E system that exhibits uncontrolled progressive DNA cleavage, a recently discovered HNH domain linked to the Cas5 subunit functions as the nuclease for precise DNA cleavage, highlighting the potential of this new Type I-E variant system as a precise genome editing tool. Here, we present five near- atomic cryo-EM (cryo-electron microscopy) structures of Candidatus Cloacimonetes bacterium Cas5-HNH/Cascade complex either bound or unbound to DNA. We revealed that the HNH domain extensively interacts with the adjacent subunits, including Cas6, Cas8 and Cas11. The related mutations of the crucial identified interactions can significantly weaken the performance of the enzyme. Upon the binding of DNA, the Cas-HNH/Cascade complex adopts a more compacted conformation with the subunits moving towards the center of the nuclease, thus activating the nuclease. We further identified four conserved cysteines that form a zinc-finger structure in the HNH domain and the mutations of these four cysteines can totally abolish the enzyme activity. Interestingly, we also discovered that the divalent ions such as zinc, cobalt and nickel down-regulate the enzyme performance by decreasing the stability of the Cascade complex. Together, our findings provide first structural insights into the assembly and activation of the Cas5-HNH/Cascade complex, opening new avenues for engineering this system for precise genome editing.

PALS1-associated tight junction (PATJ) protein is linked to metabolic disease and stroke in human genetic studies. Despite the recognized role of PATJ in cell polarization, its specific functions in metabolic disease and ischemic stroke recovery remain largely unexplored. Using a mouse model of stroke, we found post-ischemic stroke duration-dependent increase of PATJ abundance in endothelial cells. PATJ knock-out (KO) HEK293 cells generated by CRISPR-Cas9 suggest roles for PATJ in cell proliferation, migration, mitochondrial stress response, and interactions with the Yes-associated protein (YAP)-1 signaling pathway. Notably, PATJ deletion altered YAP1 nuclear translocation. PATJ KO cells demonstrated extensive transcriptional reprograming based on RNA sequencing analysis. Crucially, we identified dysregulation in genes central to vascular development, stress response, and metabolism, including RUNX1 , HEY1 , NUPR1 , and HK2 . These insights offer a new understanding of PATJ’s complex regulatory functions within cellular and vascular physiology and help lay the groundwork for therapeutic strategies targeting endothelial PATJ-mediated pathways for stroke rehabilitation and neurovascular repair.

Summary Tumor heterogeneity poses a significant challenge in combating treatment resistance. Despite Polo-like kinase 1 (PLK1) being universally overexpressed in cancers and contributing to chromosomal instability (CIN), direct PLK1 inhibition hasn’t yielded clinical progress. To address this, we utilized the synthetic dosage lethality (SDL) approach, targeting PLK1’s genetic interactions for selective killing of overexpressed tumor cells while mitigating heterogeneity-associated challenges. Employing computational methods, we conducted a genome-wide shRNA screen, identifying 105 SDL candidates. Further in vivo CRISPR screening in a breast cancer xenograft model and in vitro CRISPR analysis validated these candidates. Employing Perturb-seq revealed IGF2BP2/IMP2 as a key SDL hit eliminating PLK1-overexpressing cells. Suppression of IGF2BP2, genetically or pharmacologically, downregulated PLK1 and limited tumor growth. Our findings strongly propose targeting PLK1’s genetic interactions as a promising therapeutic approach, holding broad implications across multiple cancers where PLK1 is overexpressed.

Abstract Actin plays a crucial role in diverse physiological processes via the formation of dynamic networks that determine cellular shape and mechanical properties. De novo variants in cytoskeletal β- and γ-actin, encoded by human ACTB and ACTG1 genes, lead to a wide range of rare diseases, termed Non-Muscle Actinopathies (NMA). Variants include missense, frameshift, truncating variants up to whole gene deletions and induce diverse symptoms. So far, the high clinical variability and genotype-phenotype correlations in NMA remain largely unresolved. To address this question, we used CRISPR to insert in the C. elegans homologue act-2 gene nine de novo mutations identified in patients. Using these animal models, we performed a quantitative multiscale characterisation. We uncovered a variety of perturbations: actin network defects at the micro scale, cell scale abnormalities, morphogenesis failure, as well as weaker behavioural phenotypes. Importantly, the range of developmental defects observed correlates with the severity of patients’ symptoms. Thus, we provide evidence that a C. elegans - based approach represents a new way to investigate the mechanisms underlying NMA physiopathology or ultimately screen for therapeutic strategies.

Summary DNA base lesions, such as incorporation of uracil into DNA or base mismatches, can be mutagenic and toxic to replicating cells. To discover factors in repair of genomic uracil, we performed a CRISPR knockout screen in the presence of floxuridine, a chemotherapeutic agent that incorporates uracil and fluoro-uracil into DNA. We identified known factors, such as uracil DNA N-glycosylase (UNG), but also unknown factors, such as the N6-adenosine methyltransferase, METTL3, as required to overcome floxuridine-driven cytotoxicity. Visualized with immunofluorescence, the product of METTL3 activity, N6-methyladenosine, formed nuclear foci in cells treated with floxuridine. The observed N6-methyladenosine was embedded in DNA, called 6mA, which was confirmed using mass spectrometry. METTL3 and 6mA were required for repair of lesions driven by additional base damaging agents, including raltitrexed, gemcitabine, and hydroxyurea. Our results establish a role for METTL3 and 6mA to promote genome stability in mammalian cells, specially in response to base damage.

The utilization of electroporation for delivering the CRISPR/Cas9 system components has enabled efficient gene editing in mammalian zygotes, facilitating the development of genome-edited animals. In our study，This research focused on targeting the ACTG1 and MSTN genes in sheep, revealing a threshold phenomenon in electroporation with a voltage tolerance in sheep in vitro fertilization (IVF) zygotes. Various poring voltages near 40V and pulse durations were examined for electroporating sheep zygotes. The study concluded that stronger electric fields required shorter pulse durations to achieve the optimal conditions for high gene mutation rates and reasonable blastocyst development. The investigation also assessed the quality of Cas9/sgRNA ribonucleoprotein complexes (Cas9 RNPs) and their influence on genome editing efficiency in sheep early embryos. It was highlighted that pre-complexation of Cas9 proteins with single-guide RNA (sgRNA) before electroporation was essential for achieving a high mutation rate. The use of suitable electroporation parameters for sheep IVF zygotes led to significantly high mutation rates and heterozygote ratios. By delivering Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) to zygotes through electroporation, targeting the MSTN (Myostatin) gene, a knock-in efficiency of 26% was achieved. The successful generation of MSTN-modified lambs was demonstrated by delivering Cas9 RNPs into IVF zygotes via electroporation.

Ensuring sufficient gRNA transcript levels is critical for obtaining optimal CRISPR-Cas9 gene editing efficiency. The standard gRNA scaffold contains a sequence of four thymine nucleotides (4T), which is known to inhibit transcription from Pol III promoters such as the U6 promoter. Our study showed that using standard plasmid transfection protocols, the presence of these 4Ts did not significantly affect editing efficiency, as most of the gRNAs tested (55 gRNAs) achieved near-perfect editing outcomes. We observed that gRNAs with lower activity were T-rich and had reduced gRNA transcript levels. However, this issue can be effectively resolved by increasing transcript levels, which can be readily achieved by shortening the 4T sequences. In this study, we demonstrated this by modifying the sequences to 3TC. Although the 3TC scaffold modification did not improve editing efficiency for already efficient gRNAs when high vector quantities were available, it proved highly beneficial under conditions of limited vector availability, where the 3TC scaffold yielded higher editing efficiency. Additionally, we demonstrated that the 3TC scaffold is compatible with SpCas9 high-fidelity variants and ABEmax base editing, enhancing their editing efficiency. Another commonly used natural Cas9 variant, SaCas9, also benefited from the 3TC scaffold sequence modification, which increased gRNA transcription and subsequently improved editing activity. This modification was applied to the EDIT-101 therapeutic strategy, where it demonstrated marked improvements in performance. This study highlights the importance of shortening the 4T sequences in the gRNA scaffold to optimize gRNA transcript expression for enhanced CRISPR-Cas9 gene editing efficiency. This optimization is particularly important for therapeutic applications, where the quantity of vector is often limited, ensuring more effective and optimal outcomes.

This manuscript describes the development of an alternative method to detect active coronavirus infection, which targets negative-sense RNA, a product of active viral replication. Few diagnostic methods are capable of discriminating between replicating and non-replicating viruses, complicating decisions related to quarantine and therapeutic interventions. We propose strand-specific nucleic acid diagnostics as a means of distinguishing between active and inactive RNA virus infections and prototype a CRISPR-based lateral flow assay that specifically detects replicating coronaviruses. Such a paradigm in diagnostics could guide more effective public health measures to curb the spread of SARS-CoV-2 and other single-stranded viruses.

Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of editing systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation. Plant viruses, which naturally infect and spread to most tissues, present a promising delivery system for editing reagents. But most viruses have limited cargo capacities, restricting their ability to carry large CRISPR-Cas systems. Here, we engineered tobacco rattle virus to carry the compact RNA-guided TnpB enzyme ISYmu1 and its guide RNA. This innovation allowed transgene-free editing of Arabidopsis thaliana in a single step, with edits inherited in the subsequent generation. By overcoming traditional reagent delivery barriers, this approach offers a novel platform for genome editing, which can greatly accelerate plant biotechnology and basic research.