The intestinal mucus layer consists of secreted and transmembrane (TM) mucins expressed on the apical surface of enterocytes. The TM mucin MUC1 has a highly O-glycosylated extracellular domain (ED) and a cytoplasmic tail (CT) with signaling potential. MUC1 is a target for the Salmonella adhesin SiiE, which mediates apical invasion of the bacterium into enterocytes. Here, we determined the contributions of the MUC1 ED and CT to Salmonella invasion and subsequent host immune responses. Enzymatic removal of the MUC1 ED from HT29-MTX intestinal cultures blocked Salmonella invasion to levels comparable to MUC1 knockout cells. CRISPR-mediated targeted deletion of the MUC1 CT (MUC1-ΔCT) did not quantitatively affect Salmonella invasion. To investigate downstream host responses, RNAseq transcriptomics analysis of uninfected and Salmonella -infected MUC1-WT, MUC1-ΔCT, and ΔMUC1 cultures was performed. Deletion of full-length MUC1 greatly altered the transcriptome, while only a small group of 132 genes was differentially expressed in MUC1-ΔCT cultures during infection. Several of these CT-dependent genes are related to the NFκB pathway. Immunoblot analysis demonstrates that under uninfected conditions, expression of NFκB subunits RelB, NfkB1-p105, NfkB2-p100, and IκBα was significantly lower in MUC1-WT compared to MUC1-ΔCT and ΔMUC1 cultures. Secretion of cytokines and immune factors was severely reduced in ΔMUC1 cultures, coinciding with reduced Salmonella invasion. In MUC1-ΔCT cultures, only galectin-3 and IL-18 secretion were significantly reduced. We conclude that the MUC1 ED is essential for Salmonella invasion, while the CT modulates the canonical and non-canonical NFκB pathway, pointing at distinct roles for MUC1 domains in microbe-host interactions and signaling. Importance The intestinal mucus layer plays an important role in separating commensal and pathogenic microbes from the underlying epithelium. The transmembrane mucin MUC1 is expressed by different types of intestinal epithelial cells and is thought to have important protective and signaling functions. However, enteropathogenic Salmonella bacteria can hijack MUC1 through engagement with the SiiE adhesin which leads to bacterial invasion of enterocytes at the apical surface. In this study, we determined how the different MUC1 domains contributed to Salmonella invasion and subsequent host responses. We found that the glycosylated MUC1 extracellular domain, but not the cytoplasmic tail, is essential for bacterial invasion. In infected and uninfected intestinal cultures, the MUC1 cytoplasmic tail modulates immune responses including NFκB activation and cytokine secretion. Our study contributes to our understanding of the diverse functions of transmembrane mucins at the intestinal microbe-host interface.

Jasmonic acid (JA) is the precursor of the bioactive molecule jasmonoyl-isoleucine (JA-Ile), a plant hormone that regulates fitness and development. Although JA biosynthesis, signaling, and responses have been intensively studied, the catabolism of JA remains incompletely understood. Here, we used the recently developed technique of limited proteolysis-coupled mass spectrometry (LiP-MS) to investigate metabolite–protein interactions in plants, aiming to discover enzymes involved in JA metabolism. We identified several previously reported JA-binding proteins, thus validating the robustness of the method, along with recognized enzymes of the JA pathway and a series of novel potential JA-binding proteins. We performed functional characterization of a set of identified JA-interacting UDP-glucuronosyltransferase (UGT) enzymes through omics, biochemical, enzymatic, and structural analyses. Our results demonstrate that two tomato UGTs effectively glucosylate JA to form JA-glucosyl esters, potentially playing a role in the regulation of bioactive JA homeostasis. With this, our findings uncovered a missing step in the metabolism of JA.

ABSTRACT Heterotaxy (HTX) syndrome is a congenital disorder characterized by abnormal left-right organ placement, often leading to severe congenital heart defects (CHD). Despite advances in sequencing, many CHD/HTX-associated genes remain functionally unvalidated, hindering effective clinical diagnosis and management. Here, we leveraged a high-throughput CRISPR/Cas9 screening approach in the Xenopus model to rapidly evaluate candidate genes identified from whole-exome sequencing of human CHD patients. Our screen identified Filamin B (FLNB), an actin-binding protein previously linked to skeletal disorders but not to ciliopathies or CHD. We identified 5 probands with CHD/HTX, 3 with recessive, and 2 with damaging heterozygous mutations in FLNB. Disrupting FLNB in Xenopus reproduced key features of the human HTX phenotype, including defects in cardiac development and impaired motile cilia function. Rescue experiments confirmed the functional conservation of human FLNB, directly implicating actin cytoskeletal disruption in ciliogenesis and left-right patterning defects. Our results provide crucial evidence linking human FLNB dysfunction to ciliopathies and CHD/HTX.

CRISPR-based genetic perturbation screens paired with single-cell transcriptomic readouts (Perturb-seq) offer a powerful tool for interrogating biological systems. Yet the resulting datasets are heterogeneous—particularly in vivo —and currently used cell-level perturbation labels reflect only CRISPR guide RNA exposure rather than perturbation state; further, many perturbations have a minimal effect on gene expression. For perturbations that do alter the transcriptomic state of cells, intracellular guide RNA abundance exhibits a dose-response association with perturbation efficacy. We combine (i) per-perturbation, expression-only classifiers trained with non-negative negative–unlabeled (nnNU) risk to yield calibrated scores reflecting the perturbation state of single cells and (ii) a monotone guide abundance prior to yield a per-cell pseudo-posterior that supports both assignment of perturbation probability and selection of affected gene features. To obtain a low-dimensional representation that allows for the accurate reconstruction of gene-level marginals for counterfactual decoding, we train an autoencoder with a quantile–hurdle reconstruction loss and feature-weighted emphasis on perturbation-affected genes. The result is a perturbation-aware latent embedding amenable to downstream trajectory modeling (e.g., optimal transport or flow matching) and a principled probability of perturbation for each non-control cell derived jointly from its guide counts and transcriptome.

Basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and exhibits a recurrent large chromosomal deletion in chromosome 4p (chr4p). Chr4p loss is associated with poor survival, evolves early in tumorigenesis and confers on cells a proliferative state. Here, we map the integrated metabolic complex genetic interaction network of chr4p in basal breast cancer to identify targetable vulnerabilities. Differential gene expression analysis of patient derived xenografts and cancer cell models revealed that chr4p loss is associated with changes in cellular energetics and reduction/oxidation balance. Analysis of DepMap pooled genome-wide CRISPR-Cas9 screens identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models. Functional assays revealed that chr4p loss is associated with disrupted mitochondrial respiratory function and reduced glycolytic capacity, suggesting metabolic rewiring. Increased reactive oxygen species and lipid peroxidation compromised antioxidant defense mechanisms. Ultimately, this study sheds light on targeted therapies for basal breast cancer harboring large chromosomal deletions.

ABSTRACT CRISPR technologies has become an integral part of plant biotechnology, synthetic biology and basic plant research, routinely used by researchers for targeted genome modifications. CRISPR guide RNAs (gRNAs) undermines the highly programmable nature of CRISPR, enabling site-specific genome editing. However, different gRNA targets showed highly variable on-target effectiveness and poor gRNA design could amount to wasting valuable scientific resources. There has been broad development of computational and web-based tools for gRNA efficiency predictions but their performances in plant genome editing remains controversial or untested. Hence, in this study, we systematically evaluated over 20 accessible, web-based in silico gRNA on-target efficiency prediction tools using an experimental plant genome editing dataset. Excitingly, we identified multiple tools, mostly developed using machine learning, that were highly predictive of gRNA on-target genome editing efficiency in planta . The prediction scores assigned to gRNAs in the dataset by these tools were significantly correlated with the frequency of CRISPR-mediated InDels in plants. Furthermore, we evaluated efficiency prediction scores available on popular platforms such as CRISPOR and CRISPR-P which contain large numbers of non-model plant genomes. Our analysis showed that some prediction scores on CRISPOR performed quite well which allows efficient integration of on-target and off-target predictions. Overall, we believe that our study provided insights on improving gRNA design during conventional plant genome editing workflows and should also help unfamiliar researchers interested in CRISPR/SpCas9 genome editing.

ABSTRACT BACKGROUND Genetic susceptibility is a major determinant in intracranial aneurysm (IA) formation and rupture, yet the underlying mechanisms linking genetic variation to vascular dysfunction remain largely unknown. We have identified mutations in ARHGEF17, a guanine nucleotide exchange factor that regulates RhoA activation and cytoskeletal organization, as potential risk variants for IA. Given ARHGEF17’s regulatory role in endothelial barrier integrity and actin remodeling, we hypothesized that ARHGEF17 deficiency promotes IA pathogenesis through dysregulation of the RhoA/ROCK2/MLC signaling axis, leading to endothelial dysfunction and vascular wall instability. METHODS CRISPR–Cas9–mediated ARHGEF17 knockout (ARHGEF17 ⁻/⁻ ) mice and morpholino-based ARHGEF17-deficient zebrafish were established to assess the in vivo vascular effects of ARHGEF17 loss. An intracranial aneurysm model combining elastase injection and deoxycorticosterone acetate (DOCA)–induced hypertension was used to evaluate aneurysm incidence, rupture rate, and survival. Structural remodeling of the Circle of Willis (CoW) was assessed by Victoria Blue, EVG, and Picrosirius Red staining, as well as immunofluorescence for α-SMA, OPN, CD31, and inflammatory markers. Complementary in vitro studies were performed in HUVECs using lentiviral ARHGEF17 silencing (three shRNAs of varying efficiency) to examine endothelial proliferation, migration, tube formation, and barrier function (TEER). Activation of RhoA/ROCK2/MLC signaling was quantified by G-LISA and Western blotting. The ROCK inhibitor Y-27632 (10 μM) was applied to determine pathway dependence. RESULTS ARHGEF17 ⁻/⁻ mice exhibited a significantly higher incidence and rupture rate of intracranial aneurysms, accompanied by fragmentation of elastic fibers, loss of collagen organization, vascular smooth muscle cell dedifferentiation, and robust inflammatory activation in the CoW. Zebrafish lacking ARHGEF17 showed frequent intracranial hemorrhage and compromised vascular wall integrity, further confirming ARHGEF17’s role in cerebrovascular stability. In ECs, ARHGEF17 knockdown impaired proliferation, migration, tube formation, and barrier integrity in a silencing-efficiency–dependent manner. Mechanistically, ARHGEF17 deficiency activated the RhoA/ROCK2/MLC pathway, leading to increased phosphorylation of MLC and MYPT1 and disorganization of F-actin and junctional proteins. Pharmacological inhibition with Y-27632 restored endothelial function, normalized cytoskeletal structure, and re-established junctional continuity, indicating a ROCK2-dependent mechanism. CONCLUSIONS Our findings establish ARHGEF17 as a critical regulator of cerebrovascular integrity and identify RhoA/ROCK2/MLC mediated cytoskeletal remodeling as the mechanistic link between ARHGEF17 deficiency and aneurysm pathogenesis. Loss of ARHGEF17 compromises endothelial barrier function, triggers vascular inflammation, and promotes aneurysm formation and rupture. Importantly, ROCK inhibition rescues endothelial dysfunction, highlighting the RhoA/ROCK2/MLC axis as a promising therapeutic target for ARHGEF17 mutation–associated intracranial aneurysms.

Anopheles gambiae is one of the principal vectors of human malaria. Over the past two decades, transgenic mosquito strains have been essential tools for studying mosquito biology and developing genetic control strategies such as gene drives. Mosquito transformants are typically identified using fluorescent markers, which are assumed to be phenotypically neutral. While generating CRISPR-based gene drive strains carrying an OpIE2 -DsRed marker we unexpectedly found that transgenic females were unable to blood-feed and were consequently sterile, whereas males initially appeared normal and fertile. Given the potential utility of dominant, female-specific sterility for mosquito control, we established additional strains controlling for transgene content and integration site, confirming that the OpIE2 -DsRed cassette caused the defect. Behavioral assays showed that females exhibited normal attraction to a membrane feeder but failed to initiate blood-feeding, performing repeated cycles of probing and proboscis grooming in rapid succession before ultimately leaving the feeder unfed. Microscopy showed that both sexes possessed a distally curved proboscis, providing a morphological explanation for the blood-feeding defect of females and the reduced male lifespan. A second promoter variant ( OpIE2b ), differing in flanking sequences at the IE-2 junction, drove strong marker expression without impairing blood-feeding or longevity. These findings demonstrate that minor differences in promoter architecture can produce major, unexpected phenotypic effects. OpIE2b provides a robust, phenotypically neutral marker for An. gambiae research, while OpIE2a highlights the need for rigorous validation of transgenic components intended for research and applied releases.

Ganoderic Acid DM (GA-DM), a triterpenoid derived from Ganoderma lucidum , exhibits anti-cancer and anti-diabetic activities, but the underlying mechanisms of action remain unclear. To identify genetic modulators of GA-DM response, we conducted a genome-wide CRISPR/Cas9 knockout screen in human melanoma cells. The screen revealed key roles for genes regulating lipid metabolism and inflammatory signalling, particularly the SREBP (Sterol Regulatory Element-binding Protein) and NF-κB (Nuclear Factor kappa-light-chain-enhancer of activated B cells) pathways, in the cellular response to GA-DM. While loss of genes involved in regulation of cholesterol biosynthesis conferred resistance to GA-DM, the disruption of ubiquitin-mediated proteolysis and the Hippo pathway genes sensitised cells to GA-DM. Inflammatory genes enriched at later time points suggests that a delayed cellular response contributes to cytotoxicity. Our findings propose a mechanistic model wherein GA-DM perturbs lipid and inflammatory pathways to exert cytotoxic effects and highlights potential targets to enhance its therapeutic efficacy. This work demonstrates the utility of functional genomics in elucidating natural product mechanisms and guiding rational drug development.

Background Mavacamten, a first-in-class allosteric myosin inhibitor, has demonstrated efficacy and safety in obstructive hypertrophic cardiomyopathy (oHCM), notably reducing symptoms, left ventricular outflow obstruction, and wall thickness over 30 weeks. We recently reported that the MYBPC3 c.772G>A variant causes HCM through cMyBP-C haploinsufficiency, leading to accelerated sarcomere kinetics and higher energy consumption in patient myocardium and hiPSC- derived cardiomyocytes (hiPSC-CMs). These effects are counterbalanced by prolonged action potentials and slower Ca²⁺ transients, which preserve twitch duration but may increase arrhythmic risk. Mavacamten may reduce myocardial energetic defects in HCM. Objectives To investigate the long-term effects of Mavacamten on sarcomere structure, contractility, and transcriptional remodeling using patient-specific and CRISPR-corrected isogenic hiPSC-derived cardiomyocyte models of HCM. Methods HiPSC-CMs and engineered heart tissues (EHTs) derived from a MYBPC3:c.772G>A patient and its CRISPR-corrected line were first exposed to increasing concentrations of Mavacamten to assess acute dose–response relationships and determine IC 50 values. Based on these data, chronic treatments (0.3– 0.75 μM for 20 days) were performed mechanical, structural, electrophysiological, and transcriptomic adaptations. Results Acute exposure produced a rapid and fully reversible reduction in active force, while chronic treatment for 20 days induced a sustained decrease in contractility with incomplete recovery after 4 days of washout, indicating a two-phase mechanism of action. Long-term force reduction was paralleled by decreased cell area and sarcomere density, indicating that structural disassembly contributes to sustained functional depression and re-assembly after washout. Electrophysiological analysis confirmed the specific alterations of the MYBPC3 c.772G>A mutation previously observed, with no detectable effects following treatment with Mavacamten. In addition, transcriptome analysis was used to study the molecular mechanisms underlying the long-term effect. Conclusions Mavacamten induces a biphasic, persistent-to-reversible, reduction of sarcomeric force associated with structural remodeling, providing mechanistic insight into its capacity to promote favorable cardiac remodeling in oHCM.

Desminopathies are a heterogeneous group of myofibrillar myopathies defined by the presence of desmin-positive aggregates that compromise cytoskeletal integrity in skeletal and cardiac muscle. Although desmin knockout models and several truncating mutations typically result in a functional null phenotype without inclusion body formation, the molecular consequences of specific stop-gain variants remain poorly understood. In this study, we investigated the pathogenic mechanism of a novel DES nonsense mutation, NM_001927.4:c.448C>T; p.(Arg150Stop), previously identified in an Indian patient with congenital myopathy. This premature stop codon lies within the Linker 1A domain and is predicted to generate a truncated protein lacking the C-terminal tail. To delineate its functional consequences, we used two complementary experimental approaches: transient overexpression of the R150X mutant in skeletal and cardiac myocytes, and a CRISPR/Cas9-engineered homozygous R150X cardiomyocyte line (Des-R150X-CRISPR). Both models consistently revealed the formation of persistent aggregate-like structures, in striking contrast to desmin knockout systems that do not generate inclusions. These aggregate-like structures disrupted actin filament organization, impaired filament bundling, and induced organelle mislocalization. Biochemical analysis indicated that the aggregates were resistant to proteasomal degradation, yet they were partially cleared by autophagy, underscoring a role for protein quality control pathways in modulating disease severity. Importantly, the Des-R150X-CRISPR line demonstrated aggregate-driven pathology at endogenous levels, confirming that this mutation acts through a toxic gain-of-function mechanism rather than simple loss of desmin function. Our findings establish the Arg150Stop variant as a mechanistically distinct truncating mutation that generates aggregation-prone protein rather than a null state. By reproducing hallmark features of desminopathy in a physiologically relevant human cell models, this work not only broadens the known pathogenic spectrum of DES variants but also highlights aggregate formation as a central driver of cellular dysfunction and a promising therapeutic target in desminopathies.

Nanomedicine has now become a radical agent of change in the game of immunotherapy and introduced precision, control, and customization like never before when it comes to cancer, as well as autoimmune conditions. Using platforms based on nano scale, researchers have been able to manipulate immune responses by working on a scale both spatial and temporal in such a way that it helps overcome the drawbacks associated with working with immune response such as immune evasion, systemic toxicity and poor pharmacokinetics. Sophisticated nanoparticles (such as stimuli-sensitive ones, exosome-mimetic vesicle nanoparticles, and nanoparticles with CRISPR) allow directed immunomodulators, antigens and gene-editing systems to reach one or more particular immune compartments. The innovations allow reprogramming of immune cells, immune tolerance rejuvenation and expansion of antitumor immunity without significant off-target effects. Finding applications in integrating the artificial intelligence as well as multi-omics techniques, the process leads to personalization of the nano-immunotherapies based on patient-specific immuno-signatures. The chapter discusses the mechanistic rationale, therapeutic advancement, and the translational opportunities of nanotechnology-based immunotherapies that define them as part of a foundation of future generations of clinical approaches to precision immune modulation in oncology and autoimmune diseases.

Precision oncology is broadly defined as cancer prevention, diagnosis, and treatment specifically tailored to the patient based on his/her genetics and molecular profile. In simple terms, the goal of precision medicine is to deliver the right cancer treatment to the right patient, at the right dose, at the right time. Precision oncology is the most studied and widely applied subarea of precision medicine. Now, precision oncology has expanded to include modern technology (big data, single-cell spatial multiomics, molecular imaging, liquid biopsy, CRISPR gene editing, stem cells, organoids), a deeper understanding of cancer biology (driver cancer genes, single nucleotide polymorphism, cancer initiation, intratumor heterogeneity, tumor microenvironment ecosystem, pan-cancer), cancer stratification (subtyping of traditionally defined cancer types and pan-cancer re-classification based on shared properties across traditionally defined cancer types), clinical applications (cancer prevention, early detection, diagnosis, targeted therapy, minimal residual disease monitoring, managing drug resistance), lifestyle changes (physical activity, smoking, alcohol consumption, sunscreen), cost management, public policy, and more. Despite being the most developed area in precision medicine, precision oncology is still in its early stages and faces multiple challenges that need to be overcome for its successful implementation. In this review, we examine the history, development, and future directions of precision oncology by focusing on emerging technology, novel concepts and principles, molecular cancer stratification, and clinical applications.

The major pathological hallmarks of sporadic and familial forms of Parkinson’s disease (PD) are the targeted and progressive loss of midbrain dopaminergic neurons (mDA), associated with systemic iron accumulation, α-synuclein (αsyn) accumulation and aggregation, and lipid peroxidation amongst other reactive oxygen species (ROS) generation. Therapeutic strategies aimed towards dopamine restoration, αsyn removal and iron chelation have provided symptomatic relief but failed to prevent or slow disease progression. This is in part due to the lack of understanding of the exact pathways leading to neuronal death in PD. In this study, we investigate ferroptosis, a unique cell death mechanism sharing multiple features with PD pathology, as a relevant pathway with implications in disease pathogenesis. We identified an enrichment of ferroptosis genes dysregulated throughout PD postmortem brain samples and several neuronal and glial PD models. Using CRISPR/Cas9 technology, we generated a rapid iPSC-derived synucleinopathy neuronal model harbouring the SNCA A53T mutation and report increased ROS generation, reduced levels of antioxidant glutathione (GSH), impaired mitophagy and a heightened vulnerability to ferroptosis-induced lipid peroxidation and cell death. Critically, inhibition of the key lipid peroxidation enzyme and driver of ferroptosis, 15-lipoxygenase (15-LO), rescued synucleinopathy associated pathologies and prevented pathological αsyn oligomerisation in SNCA A53T neurons. Furthermore, we report enhanced microglial ferroptosis susceptibility in models of synucleinopathy. In summary, we highlight a new mechanism by which the familial PD-associated SNCA A53T mutation causes cell death and propose 15-LO inhibition as a tractable therapeutic opportunity in PD.

ABSTRACT Understanding the molecular mechanisms by which erythropoietin (EPO) acts as neurotrophic factor that enhances hippocampal function and learning is essential to harness its therapeutic potential. Here, we employ single-nucleus ATAC-seq and RNA-seq to map the epigenomic and transcriptional landscapes of adult mouse hippocampus under recombinant human EPO (rhEPO) treatment. We discover significant lineage-specific chromatin remodeling predominantly in newly formed and immature excitatory neurons, highlighting a robust EPO-driven neurogenic response as the first direct evidence that an extrinsic factor can induce adult hippocampal neurogenesis. Notably, many EPO-induced accessible regions overlap ancient transposable elements, particularly ancient LINEs and SINEs, that are bound by key neurogenic transcription factors such as NEUROD1/2, NEUROG2, FOXG1, and ASCL1 and are linked to nearby genes governing neuronal differentiation and synaptic plasticity. Our findings uncover a previously unrecognized transposon-mediated mechanism underlying EPO-induced neurogenesis, highlighting an underappreciated role for TE-derived sequences in this process, and establish a publicly available single-nucleus multiomic atlas as a resource for understanding cell-type-specific gene regulation and neuroplasticity in the adult brain.

Background Antimicrobial resistance (AMR) in Escherichia coli is a critical global health challenge, particularly in urinary tract infections, where first-line treatments are increasingly compromised. While horizontal gene transfer (HGT) via mobile genetic elements is a major driver of AMR, the genomic factors that may constrain resistance gene acquisition remain underexplored. CRISPR-Cas systems, which provide adaptive immunity against foreign DNA, could influence AMR dynamics, but their role in E. coli remains incompletely understood. Methods We conducted a comprehensive whole-genome analysis of uropathogenic E. coli isolates, including a newly sequenced collection from Australian clinical samples and an independent, globally sourced validation cohort. Antimicrobial susceptibility profiles were integrated with CRISPR-Cas subtype classification, resistance gene burden, and mobile element content. Elastic net regression, adaptive lasso, and tree-based machine learning models were used to identify genomic predictors of resistance, with performance validated across both datasets. Results CRISPR-Cas subtype I-F was consistently associated with susceptibility to antibiotics commonly acquired through HGT, including trimethoprim and ampicillin, and linked to lower ARG and MGE burden. In contrast, Type I-E arrays, especially when co-occurring with orphan I-F arrays, were associated with increased resistance. These associations remained robust after adjusting for phylogroup, plasmid content, and genomic background, and were validated across datasets. Conclusions Subtype-specific CRISPR-Cas systems shape antibiotic resistance profiles in E. coli , with Type I-F functioning as a potential genomic barrier to ARG acquisition. These findings highlight CRISPR array typing as a novel biomarker for AMR risk prediction and surveillance, and suggest new opportunities for leveraging CRISPR-based mechanisms to limit resistance propagation in clinical contexts.

Abstract Horizontal gene transfer (HGT) is a major driver of microbial evolution, yet the influence of host cellular context on the integration and functionality of transferred genes remains underexplored. In this study, we investigate how host background affects the compatibility and consequences of acquiring post-translational modification (PTM) machinery through HGT using the heterologous expression of the highly conserved translational elongation factor P (EF-P) from diverse species in Escherichia coli as a model. EF-P and its PTM machinery have been horizontally transferred many times across the bacterial tree of life, and these experiments are meant to examine the consequences of these events. EF-P has a diverse and heterogenous relationship with PTMs; three characterized variants each undergo distinct PTM pathways, while others function effectively without any modification. In this study, we demonstrate that EF-P from Deinococcus radiodurans , Geoalkalibacter ferrihydriticus , and Nitrosomonas communis can complement an EF-P knockout in E. coli without requiring modification, suggesting they represent new examples of unmodified EF-Ps. We also found that the EF-P from the Thermotogota Mesotoga prima is post-translationally modified in an off-target reaction by the rhamnosylation enzyme EarP, thus interfering with its functionality. Conversely, we saw that rhamnosylation by EarP is fully compatible with the EF-P-like protein EfpL from Escherichia coli , thus presenting a promising opportunity to develop novel, catalytically active PTMs. These findings highlight that PTM systems introduced via HGT can have unintended effects on host proteins, emphasizing the complexity of gene integration and functional compatibility in foreign genomic contexts.

Abstract Among microbially derived metabolites that influence host disease, colibactin garners increasing attention for its roles in the rising incidence of early-onset colorectal cancer. Produced by pks⁺ Escherichia coli, colibactin is a potent genotoxin, yet no approved therapeutics directly suppress it. Here, we engineered a self-transmissible conjugative plasmid to deliver CRISPR interference (CRISPRi) into multiple pks⁺ strains. This system silences transcription of colibactin biosynthetic genes and abolishes pks⁺ E. coli genotoxicity without the resistance mutations associated with wild-type Cas9-mediated bacterial inhibition. In mice, conjugation-mediated CRISPRi reduces DNA damage and pks⁺ E. coli colonization while preserving commensal diversity. Importantly, the system also lowers tumorigenesis driven by pks⁺ E. coli and outperforms a pharmacologic inhibitor in a mouse colorectal cancer model. Finally, we extend this platform to silence a second pathogenic metabolite, establishing a translational strategy to neutralize diverse microbial metabolites and expanding the toolkit for programmable live biotherapeutics in the gut.

Abstract The transition from well-fed to food-deprived conditions in C. elegans triggers a stereotypic exploration behaviour in C. elegans characterised by a temporal decrease in cumulative reorientations. We conducted a screen of neuropeptide mutants and identified several candidates involved in modulating this behaviour. Among these, the neuropeptide FLP-15 emerged as a key regulator. Our observations revealed that FLP-15 regulates the frequency of reversals during foraging through the I2 pharyngeal neuron via the G-protein coupled receptor NPR-3. Mutants lacking either flp-15, npr-3 or both displayed a significant defect in reversal frequency which did not decline temporally unlike in wild-type animals. This study also describes the expression pattern of NPR-3 in a subset of head neurons, predominantly comprising of dopaminergic neurons. Finally, flp-15 expression studies and exogenous dopamine supplementation assays revealed that FLP-15 may regulate exploratory search by modulating dopamine transmission, highlighting a novel neuropeptide-dopamine interaction involved in the control of foraging behaviours.

Staphylococcus aureus remains a major clinical threat due to rising antibiotic resistance and high rates of treatment failure. Deciphering the genetic responses to antibiotic pressure and identifying conserved vulnerabilities are essential steps toward developing broadly effective therapies. Here, we constructed strain-resolved CRISPR interference (CRISPRi) libraries targeting all genes in four clinically relevant S. aureus strains spanning major clonal complexes. CRISPRi-seq screens enabled high-resolution mapping of their fitness landscapes and the definition of a core essentialome representing robust targets for antimicrobial intervention. Exposure of the CRISPRi libraries to four mechanistically distinct antibiotics revealed genome-wide susceptibility profiles, identifying both strain-dependent and conserved susceptibility signatures shaped by the drug mode of action and genetic background. Analysis of these conserved vulnerabilities provided insight into antibiotic-specific stress responses and resistance mechanisms. Among the core determinants of vancomycin vulnerability, we identified several previously uncharacterized genes, including a conserved membrane-associated operon, here designated EsrABC, whose disruption markedly increases vancomycin sensitivity in the four strains. Our study provides a genome-wide atlas of S. aureus fitness and conditional vulnerabilities, fully explorable in the here-developed online AureoBrowse platform ( https://aureobrowse.veeninglab.com/ ), revealing candidates for synergistic therapies and potential therapeutic targets.

Autophagy (cellular self-eating) is a tightly regulated catabolic process of eukaryotic cells in which parts of the cytoplasm are sequestered and subsequently degraded within lysosomes by acidic hydrolases. This process is central to maintaining cellular homeostasis, the removal of aged or damaged organelles, and the elimination of intracellular pathogens. The nematode Caenorhabditis elegans has proven to be a powerful genetic model for investigating autophagy. To date, the fluorescent autophagy reporters developed in this organism have predominantly relied on multi-copy, randomly integrated transgenes. As a result, the interpretation of autophagy dynamics in these models has required considerable caution due to possible overexpression artifacts and positional effects. Here, we describe the development of two endogenous autophagy reporters, engineered using CRISPR-Cas9 genome editing: gfp::mCherry::lgg-1/atg-8 and gfp::atg-5, both inserted precisely into their endogenous genomic loci. These single-copy reporters reliably track distinct stages of the autophagic process. Using these tools, we demonstrate that (i) the transition from the earliest phagophore to the mature autolysosome is an exceptionally rapid event, (ii) starvation triggers autophagy only after a measurable lag phase, rather than immediately, and (iii) autophagy in C. elegans is subject to strict regulatory control, preventing excessive flux that could otherwise compromise cellular survival. We anticipate that these newly developed reporter strains will provide refined opportunities to dissect the physiological and pathological roles of autophagy in vivo.

We present a platform that directly sequences single guide RNAs and endogenous 3′UTRs in fixed cells while simultaneously measuring protein abundance and cellular morphology. We demonstrate platform capability by performing optical pooled screening of CRISPR-perturbed lung cancer cells. This approach unites direct in-sample RNA sequencing with complementary phenotypic readouts, enabling comprehensive, scalable, and functional genomics analyses within a single experiment.

Attaching effacing (A/E) bacteria, such as Enteropathogenic E. coli (EPEC) and Citrobacter rodentium , colonize intestinal epithelial cells (IECs) by inducing remodeling of the epithelial cytoskeleton and formation of prominent actin pedestals at bacterial attachment sites. While non-muscle myosin II (NM II) is a key regulator of the actin cytoskeleton, whether it regulates IEC colonization by A/E pathogens is not known. To address this question, we targeted NM IIA and NM IIC, the NM II paralogs expressed in IECs. Our in vivo studies utilized mouse models with either intestinal epithelial-specific deletion of NM IIA (NM IIA cKO mice), expression of a NM IIA motor domain mutant, or total deletion of NM IIC (NM IIC tKO mice). In vitro experiments utilized IECs (HT-29cF8 and Caco-2BBE) with CRISPR-Cas9-mediated deletion of NM IIA or NM IIC. In addition, NM II activity in vitro was modulated pharmacologically, using either the pan-myosin inhibitor, blebbistatin, or a specific NM IIC activator, 4-hydroxyacetophenone (4-HAP). NM IIA cKO and NM IIA mutant mice demonstrated higher C. rodentium colonization along with more severe mucosal inflammation and colonic crypt hyperplasia as compared to their controls. By contrast, NM IIC tKO mice was indistinguishable from their control with regard to C. rodentium colonization. Blebbistatin treatment increased EPEC attachment to IECs monolayers, whereas 4-HAP did not affect bacterial attachment. Genetic knockout of NM IIA, but not NM IIC, increased EPEC adhesion to IEC monolayers. Importantly, the increase in EPEC attachment exhibited by NM IIA-deficient IECs required intact bacterial Type 3 secretion system and functional Tir effector, indicating that NM IIA functions in actin pedestal assembly. In summary, we describe a novel role for NM IIA in limiting intestinal epithelial colonization by A/E pathogens via inhibition of pathogen-induced remodeling of the actin cytoskeleton.

Summary Microglia, the brain’s innate immune cells, can adopt a wide variety of activation states relevant to health and disease. Dysregulation of microglial activation occurs in numerous brain disorders, and driving or inhibiting specific states could be therapeutic. To discover regulators of microglial activation states, we conducted CRISPR interference screens in iPSC-derived microglia for inhibitors and activators of six microglial states. We identified transcriptional regulators for each of these states and characterized 31 regulators at the single-cell transcriptomic and cell-surface proteome level in two distinct iPSC-derived microglia models. Finally, we functionally characterized several regulators. STAT2 knockdown inhibits interferon response and lysosomal function. PRDM1 knockdown drives disease-associated and lipid-rich signatures and enhanced phagocytosis. DNMT1 knockdown results in widespread loss of methylation, activating negative regulators of interferon signaling. These findings provide a framework to direct microglial activation to selectively enrich microglial activation states, define their functional outputs, and inform future therapies. Highlights CRISPRi screening reveals novel regulators of six microglia activation states Multi-modal single-cell screens highlight differences between mRNA and protein level expression iPSC-microglia models show different baseline distributions of activation states Loss of DNMT1 leads to widespread DNA demethylation, promoting some states but limiting the interferon-response state Loss of PRDM1 drives microglial disease-associated state

In early 2025, Sierra Leone experienced a large outbreak of mpox clade IIb, underscoring the urgent need for portable, low-cost diagnostics in decentralized settings. We rapidly developed and field-deployed Mpox SHINE, a CRISPR–Cas13 assay that integrates lyophilized reagents, ambient-temperature lysis, and automated fluorescence detection on a portable device, the DxHub. The assay achieved analytical sensitivity down to 10 copies/µL with minimal hands-on time. In-country evaluation of 56 clinical specimens showed complete concordance with qPCR, with 100% sensitivity (45/45) and 100% specificity (11/11) at the sample level. Mpox SHINE also detected the virus directly from unextracted lesion swabs, maintaining 100% sensitivity and specificity in 16 samples (8 positive, 8 negative). Across extracted and unextracted samples, the mean time-to-result was ∼35 minutes, with all positives detected within 45 minutes. Thus, Mpox SHINE performed on the DxHub demonstrates how CRISPR-based pathogen detection can be rapidly translated into portable tools for the front lines of outbreak response. Teaser CRISPR-Cas13 assay and portable device bring rapid, reliable mpox testing to outbreak settings.