Summary Cancer cells reprogram metabolism to fuel aggressive growth and resist therapies, yet mapping these metabolic changes remains a major challenge. While constraint-based genome-scale models describe steady states, kinetic models that resolve time-dependent fluxes and metabolite concentrations in human cancers are rare. Here, we integrate multi-omics data and physicochemical constraints to construct large-scale kinetic models of ovarian cancer metabolism that capture how tumor cells adapt their nutrient use and energy production. Comparing ovarian cancer cells with and without BRCA1 loss revealed distinct metabolic strategies driven by transcriptional regulation. The models reproduce hallmark phenotypes, correctly predict known metabolic drug targets, and identify previously uncharacterized vulnerabilities in nucleotide and lipid synthesis. Simulations of drug treatments mirror clinical responses and consistently reveal a ceramide-linked stress signature common to many chemotherapies. Using the same framework, we show that BRCA1 loss redirects metabolic pathway activity through enzyme activity changes linked to transcription factors interacting with BRCA1 , suggesting regulatory routes for network-level rewiring. By capturing dynamic fluxes and concentrations, these models bridge molecular insight with therapeutic action, guiding biomarker discovery and dosing strategies. This open-access resource provides a mechanistic foundation for testing metabolic interventions, deepening our understanding of cancer metabolism across tumor types, and advancing the promise of precision oncology.

Pooled CRISPR screening combined with single-cell RNA sequencing (scRNA-seq) has emerged as a powerful strategy for dissecting gene function and reconstructing gene regulatory networks (GRNs) in complex biological systems. This approach enables high-throughput, parallel perturbation of multiple genes while providing transcriptome-wide readouts at single-cell resolution, overcoming many limitations of traditional arrayed screens. However, its broader application remains limited by technical challenges, including variable perturbation efficiency and difficulties in accurately identifying perturbed cells. In this study, we adapted and applied a modified CRISPR droplet sequencing (CROP-seq) protocol using CRISPR interference (CRISPRi) in K562 cells to knockdown six transcription factors (TFs): LMO2, TCF3, LDB1, MYB, GATA2, and RUNX1. Our modified approach, which allows direct capture of sgRNAs from the cDNA library without a separate enrichment step, significantly improved sgRNA assignment per cell. We successfully achieved reproducible knockdown of three TFs (MYB, GATA2, and LMO2), captured the impact of these perturbations on the TF target genes, and enabled us to reconstruct their GRNs and identify key regulons and transcriptional targets. These networks revealed both previously established (such as LMO2 GATA2 interaction) and novel regulatory interactions, which we independently validated, providing new insights into hematopoietic transcriptional control. To assess the efficiency of CRISPRi based pooled perturbation, we additionally analyzed publicly available pertrub-seq CRISPRi datasets and found that only ∼40–50% of targeted genes led to effective knockdown, underscoring the variability in perturbation efficiency across experiments. Together, our results demonstrate both the potential and the current technical limitations of pooled CRISPRi-based single-cell screens. While this integrated approach holds great promise for high-resolution functional genomics, further optimization and standardized benchmarking are essential to improve its reliability, scalability, and reproducibility.

Abstract Muscle regeneration is governed by a complex interplay between immune cells and satellite cells (muscle progenitors), orchestrated by signaling molecules of the TGF-β superfamily. Among these, the role of GDF11 activity in skeletal muscle remains contentious, with conflicting evidence suggesting both stimulatory and inhibitory effects. This functional divergence may emerge from the combinatorial activities of its shared type I receptors and context-dependent activation of downstream SMADs. To dissect the role of GDF11 in skeletal myogenesis, we employed a combination of biochemical stimulation and CRISPR-based genetic approaches in chicken or human myoblasts. Analysis of cell proliferation, differentiation, adhesion, and migration revealed that GDF11 does not affect myoblast proliferation or adhesion, but strongly inhibits myotube differentiation and myoblast migration. Furthermore, loss of ACVR1B (ALK4) strongly delays myoblast differentiation, and impairs cell adhesion and migration on laminin-111 (LM111), a known ligand of the integrin VLA-6. Notably, flow cytometry phenotyping demonstrated that ACVR1B -deficient myoblasts exhibit reduced surface levels of the integrin α6 subunit (CD49f) compared to wild-type cells. Together, our findings suggest a GDF11-independent ALK4/VLA6/LM111 axis governing skeletal myoblast adhesion and fusion. Knowledge of these receptor interactions is critical for understanding GDF11’s paradoxical role in muscle cell biology and may inform novel therapeutic strategies to counteract skeletal muscle degeneration and age-related decline.

Fungal pathogens represent a major constraint to global agricultural productivity, causing a wide range of plant diseases that severely affect staple crops such as cereals, legumes, and vegetables. These infections result in substantial yield losses, deterioration of grain and produce quality, and significant economic impacts across the entire agri-food sector. Among phytopathogens, fungi are considered the most destructive, causing a wide range of diseases such as powdery mildew, rusts, fusarium head blight, smut, leaf spot, rots, late blight, and other fungal pathogens. Traditional plant protection methods do not always provide long-term effectiveness and environmental safety, which requires the introduction of innovative approaches to creating sustainable varieties. CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats) technology opens up new opportunities for targeted genome editing, allowing the modification or silencing of susceptibility genes and thus increasing plant resistance to fungal infections. This review presents current achievements and prospects for the application of CRISPR-Cas technology to increase the resistance of major agricultural crops to fungal diseases. The implementation of these approaches contributes to the creation of highly productive and resistant varieties, which is crucial for ensuring food security in the context of climate change.

Next-generation drug discovery and functional genomics require rapid, unbiased single-cell profiling at scale—demands that exceed the limited speed, throughput, and labor-intensive labeling constraints of conventional high-content image-based screening. We introduce spinning arrayed disk (SpAD), a high-throughput, label-free imaging platform for live-cell imaging that integrates continuous circular scanning, ultrafast quantitative phase imaging (QPI), and a novel circular array of 96 culture chambers. SpAD achieves an order-of-magnitude reduction in imaging time compared to traditional fluorescence-based workflows, while remaining compatible with standard cell culture workflows. By extracting rich biophysical features using intrinsic morphological (InMorph) profiling and machine learning, SpAD enables sensitive, large-scale screening of drug responses and CRISPR gene knockouts without labeling. Critically, label-free biophysical readouts from SpAD reveal mechanism-linked changes in mass, refractive index, subcellular textures, and light scattering that fluorescent labels often obscure. SpAD thereby resolves subtle phenotypes and heterogeneous subpopulations with high reproducibility, providing a robust, scalable foundation for precision cellular morphological assays.

The endogenous opioid system is a powerful modulator of motivation and affect. The dorsal raphe nucleus (DRN) in the midbrain has been established as an important site of opioid action and is an integral hub in behavioral modulation. To investigate the functional significance of DRN opioid signaling in aversive and appetitive behaviors we disrupted preproenkephalin (Penk) in DRN using CRISPR-Cas9 technology in Penk-Cre mice. We found that CRISPR mediated knockdown of enkephalin peptide in the DRN (DRN Penk ) enhanced inflammation-induced mechanical sensitivity and odor avoidance. Additionally, loss of DRN Penk diminished sucrose preference and engagement with a novel social stimulus. To further characterize the opioid system within the DRN, we performed Hiplex in situ hybridization of 12 genes in the same tissue. This revealed that DRN Penk is largely separate from DRN serotonin cells and is instead distributed on glutamatergic and GABAergic cells. However, subtype-specific knockdown of DRN Penk from glutamatergic and GABAergic cells did not replicate the behavioral effects of general DRN Penk knockdown. This suggests that these neurons represent a novel population that mediate motivated behaviors distinctly from canonical DRN mechanisms.

Abstract Gene expression during cellular differentiation is coordinated by combinatorial interactions between transcription factors (TFs) and cofactors at promoters and enhancers. The “master TF” GATA1 coordinates gene transcription in a subset of hematopoietic lineages, including erythroid, megakaryocytic, mast, and eosinophil, while repressing the development of other blood lineages. However, the specific cofactors required for GATA1-activated gene expression during hematopoiesis are incompletely defined. We identified the cofactor KMT2D, an H3K4 methyltransferase that collaborates with H3K27 acetyltransferases to activate transcription, in an unbiased CRISPR/Cas9 screen for epigenetic regulators of erythropoiesis. Loss of KMT2D in human erythroid precursors caused developmental arrest with impaired expression of numerous erythroid genes. Mechanistically, KMT2D colocalized with GATA1 on more than one thousand erythroid enhancers associated with over two hundred erythroid genes. In general, co-occupancy of GATA1 and KMT2D at erythroid enhancers was associated with stronger transcriptional activity than occupancy by GATA1 alone. Acute depletion of KMT2D in erythroid precursors caused rapid reductions of H3K4me1 and H3K27ac on a subset of GATA1-bound enhancers and impaired the expression of canonical erythroid genes, including ZFPM1, SLC4A1 , and EPOR . Moreover, acute depletion of GATA1 or KMT2D individually caused downregulation of overlapping gene sets. Thus, KMT2D controls erythropoiesis by selectively activating GATA1-dependent erythroid enhancers. Our studies identify KMT2D as a novel cofactor for transcriptional activation by GATA1 during erythropoiesis. More generally, our findings demonstrate how a lineage-specific TF cooperates with a ubiquitous epigenic regulator to drive lineage-specific gene expression during cellular differentiation.

Deciphering the functionality of the noncoding genome which includes important cis -regulatory elements (CREs) and transcribed noncoding RNA genes remains technically challenging. Here, using massively parallel genetic screening, we systematically benchmark the performance of five representative loss-of-function perturbation tools, including single guide RNA (gRNA) mediated SpCas9 cleavage or CRISPR interference, and paired gRNA (pgRNA) involved dual-SpCas9, Big Papi (paired SpCas9 and SaCas9) or dual-enAsCas12a fragment deletion methods, in decoding the roles of the noncoding genome. For targeting CREs such as enhancer, dual-SpCas9 outperforms other methods with superior efficiency of destroying functional genomic regions. For perturbing noncoding RNA genes, in addition to dual-SpCas9, other RNA-targeting methods such as RNA interference are recommended to discriminate transcript-dependent or -independent roles. A deep learning model DeepDC with associated web server is built to facilitate optimal dual-SpCas9 pgRNA design for efficiently deleting a genomic fragment. Together, our work provides practical guidance on selecting appropriate loss-of-function tools to resolve the functional complexity of the noncoding genome.

ABSTRACT Transcriptional regulation is mediated by enhancers, yet how genetic perturbations alter enhancer activity and gene expression remains poorly understood. We developed UDI-UMI-STARR-seq, which integrates dual indexes and unique molecular identifiers, and combined it with RNA-seq to profile the effects of perturbations on enhancer activity and target gene expression. We applied this approach to a library of 253,632 fragments representing 46,142 cell type–specific candidate enhancers and assessed the impact of CRISPR/Cas9-mediated deletion of six transcription factors (or TFs; ATF2, CTCF, FOXA1, LEF1, TCF7L2, and SCRT1) with diverse regulatory roles. Across knockout lines, we identified responsive enhancers that were either repressed or induced, often through motifs such as the p53 family of TFs. Enhancer–gene mapping revealed TF-specific programs, including repression of Wnt/p53 targets with ATF2 or LEF1 loss, downregulation of the FIRRE locus with CTCF loss, and compensatory upregulation of RNA polymerase II regulators following FOXA1 depletion. A deep learning model trained on enhancer sequences recapitulated core principles of enhancer grammar, including cooperative motif syntax and the influence of flanking sequence context. Applying this framework to the neurodevelopmental disorder-associated 16p12.1 deletion identified responsive enhancers linked to genes involved in axon guidance, synaptic plasticity, and translational control, providing a scalable readout of enhancer dynamics generalizable to genetic mutations.

Abstract Some childhood cancers can arise in utero and then regress at birth, but the cues that permit malignant proliferation in utero as opposed to postnatal life are often unclear. Transient abnormal myelopoiesis (TAM) is a human fetal liver leukemia driven by GATA1s mutations and a rare exemplar of a spontaneously resolving cancer when blood formation shifts from liver to bone marrow (BM) during development. Here we show that the cytokine receptor CSF2RB is aberrantly upregulated in TAM cells because it is a GATA2 target that escapes repression by GATA1s. Pathologically expressed CSF2RB unexpectedly interacts with the thrombopoietin receptor MPL to prolong JAK-STAT signaling by fetal-liver produced THPO, driving GATA1s-mutant cell expansion. TAM can transform into myeloid leukemia of Down syndrome (ML-DS) upon acquisition of additional mutations. We further show that the ML-DS driver CSF2RB A455D forces MPL dimerization resulting in constitutive JAK-STAT activation, bypassing THPO dependence in the fetal-liver niche, thereby enabling proliferation in the BM. Conversely, base-editing reversion of another ML-DS JAK-STAT-activating mutation, JAK3 A572V, restores THPO dependence. These results identify a cytokine gate that developmentally restricts GATA1s oncogenic competence, reconciling why TAM expands in the fetal liver yet resolves after birth, revealing a niche-specific, therapeutically targetable dependency.

Abstract MHC-II molecules are traditionally restricted to professional antigen-presenting cells (pAPCs), but increasing evidence highlights their expression in cancer cells, where they are associated with enhanced immune infiltration and improved clinical outcomes. However, the mechanisms governing cancer cell-intrinsic MHC-II expression remain poorly understood. Here, through genome-wide CRISPR-Cas9 screening in human melanoma cells, we identify the aryl hydrocarbon receptor (AHR) and its dimerization partner (ARNT) as critical, ligand-responsive regulators of MHC-II expression. Our analyses reveal that AHR–ARNT promotes transcription of the MHC-II transactivator CIITA through direct binding to its promoter II (pII), independently of IFN-γ signaling. Clinically, an AHR–ARNT loss-of-function signature correlates with reduced immune infiltration, poor response to immunotherapy, and inferior survival across cancer types. Together, our findings uncover a previously unrecognized, tumor-intrinsic regulatory axis of MHC-II expression and suggest that targeting the AHR–ARNT pathway may enhance tumor immunogenicity and improve responses to immunotherapy.

Predatory bacteria are abundant in soil, but their diversity and functions remain not fully understood, especially in subarctic regions. Here, we report strain 1-FT3.2, a predatory bacterium obtained from peatland soil in Northern Finland (Pallas, 68 °N). The bacterium was cultivated on Mucilaginibacter cryoferens FT3.2 as prey. Although a pure culture of strain 1-FT3.2 was not obtained, its draft genome was assembled from sequencing reads derived from the co-culture with its prey. The draft genome of 1-FT3.2 is 7.2 Mb in length and 81% complete. Genome analyses suggested that 1-FT3.2 belongs to the family Polyangiaceae (phylum Myxococcota ), which comprises predatory bacteria. The genome annotation revealed (near-)complete metabolic modules of central carbon metabolism and aerobic respiration. Two proviral regions were predicted in the draft genome, both putatively representing tailed phages of the class Caudoviricetes. Several CRISPR-Cas system proteins were also identified. The draft genome sequence could be used in future comparative studies assessing the diversity of predatory bacteria in northern soils or other environments.

Background Linking genetic perturbations to cellular phenotypes remains a central challenge in translational biology. Experimental iPSC and organoid models are powerful but constrained by scalability, variability, and difficulty modeling rare or polygenic states. Methods We developed aiAtlas v1.2 , a high-fidelity simulation platform that integrates Large Concept Model (LCM) logic with aiPSC-derived modeling. We evaluated 136 virtual cell lines spanning wild-type, single-mutation, multiple-mutation, human tumor-derived, and gene-fusion cohorts. Twenty-five features covering DNA damage/repair, replication stress, epigenetic remodeling, pluripotency, and stress responses were quantified. Statistical analysis used the Mann–Whitney U test with Bonferroni correction, Hodges–Lehmann estimators (HLE) for median differences, and Cliff’s delta effect sizes with bootstrap 95% confidence intervals . Robustness measures included early stopping, bagging, and 5-fold cross-validation. Results aiAtlas v1.2 reliably separated wild-type and mutant cohorts , revealing consistent disruptions in DNA damage accumulation, replication stress, epigenetic dysfunction, and loss of pluripotency, while identifying stable features (e.g., core nucleotide-excision repair processes and selected apoptosis measures). Subgroup analyses showed shared systemic effects and context-specific vulnerabilities : single mutations frequently produced measurable divergence; multiple mutations amplified instability; tumor-derived and gene-fusion lines yielded distinct but partially overlapping phenotypes. Large effect sizes (Cliff’s δ) with narrow bootstrap CIs supported reproducibility across cohorts. Conclusions/Impact aiAtlas v1.2 provides a robust virtual subject framework that uses aiCRISPR-Like (aiCRISPRL) virtual gene editing system that complements wet-lab CRISPR models by scaling to diverse genomic contexts and highlighting both disruption and stability. The platform can guide therapeutic prioritization, gene-editing strategy design, and regulatory innovation consistent with the FDA Modernization Act 2.0 , accelerating therapy development in rare diseases and cancer. Significance Statement aiAtlas introduces a scalable, reliable simulation framework that integrates advanced large concept model (LCM) logic with iPSC-derived cellular modeling. aiAtlas overcomes major limitations of experimental systems by capturing both broad and subgroup-specific phenotypic divergence across single mutations, multiple mutations, tumor-derived cell lines, and gene fusions. This reliable platform establishes a new opportunity for rare diseases and cancer modeling, offering reproducible insights that can accelerate discovery and translational applications where traditional wet-lab approaches are impractical. Furthermore, in situations where the target mutational profile has been defined but no cellular models yet exist, aiAtlas can quickly generate custom virtual cell lines that accurately reproduce the corresponding genomic and phenotypic features.

Incompletely understood mechanisms serve to maintain Epstein-Barr virus (EBV) latency in most B-cell states, in which viral oncogene(s) are expressed but lytic antigens are repressed. Shortly after EBV’s discovery and even before it was named, early pioneers Werne and Gertrude Henle identified that restriction of extracellular arginine de-represses EBV lytic antigens within Burkitt lymphoma tumor cells. However, for nearly 60 years, it has remained unknown how arginine metabolism supports EBV latency. To gain insights, we performed an amino acid restriction screen in Burkitt cell lines. This confirmed that arginine restriction was sufficient to trigger EBV reactivation in Burkitt B-cells and gastric carcinoma models. Arginine restriction strongly impaired de novo pyrimidine biosynthesis, and CRISPR or chemical genetic blockade of pyrimidine biosynthesis enzymes induced EBV immediate early and early lytic gene expression. However, arginine restriction blocked EBV lytic DNA replication and consequently also late gene expression, suggesting an abortive lytic cycle. Arginine restriction triggered DNA damage, which was an important driver of arginine restriction-driven EBV reactivation. Arginine restriction and DNA hypomethylation synergistically increased EBV reactivation. Together, our results highlight arginine and pyrimidine metabolism as potential targets for EBV lytic antigen induction therapy in B and epithelial cell contexts. Importance Altered metabolism is a hallmark of cancer, frequently increasing transformed cell dependence on extracellular amino acid supply. Despite current interest in EBV lytic antigen induction therapy, in which viral lytic reactivation sensitizes tumors to the highly cytotoxic effects of the antiviral ganciclovir, there has been no systemic study of extracellular amino acid that controls EBV latency. We identified that arginine uptake was important for the maintenance of EBV latency in both Burkitt lymphoma and gastric carcinoma contexts. Metabolic pathway analyses highlighted that arginine uptake and metabolism was required to supply pyrimidines. Disruption of arginine metabolism or de novo pyrimidine synthesis caused DNA damage. As arginine restriction was also found to cause Burkitt DNA hypermethylation, we provide evidence that the combination of arginine restriction and DNA hypomethylation by decitabine or by CRISPR approaches together induced EBV reactivation more highly than either alone, suggesting a therapeutic approach.

Quantitative analysis in bacterial microscopy is often hindered by diverse cell morphologies, population heterogeneity, and the requirement for specialised computational expertise. To address these challenges, mAIcrobe is introduced as an opensource framework that broadens access to advanced bacterial image analysis by integrating a suite of deep learning models. mAIcrobe incorporates multiple segmentation algorithms, including StarDist, CellPose, and U-Net, alongside comprehensive morphological profiling and an adaptable neural network classifier, all within the napari ecosystem. This unified platform enables the analysis of a wide range of bacterial species, from spherical Staphylococcus aureus to rod-shaped Escherichia coli , across various microscopy modalities within a single environment. The biological utility of mAIcrobe is demonstrated through its application to antibiotic phenotyping in E. coli and the identification of cell cycle defects in S. aureus DnaA mutants. The modular design, supported by Jupyter notebooks, facilitates custom model development and extends AI-driven image analysis capabilities to the broader microbiology community. Building upon the foundation established by eHooke, mAIcrobe represents a substantial advancement in automated and reproducible bacterial microscopy.

Translational challenges in neuroscience originate from species-specific differences that limit the generalizability of experimental findings. Comparative approaches can help distinguish conserved from species-specific mechanisms, but their application has been limited by the lack of molecular tools beyond traditional model organisms, complicating direct comparisons of conserved and divergent mechanisms of neural function. This gap is particularly evident for the dopaminergic system, a key regulator of motivated behaviors across species and the principal pharmacological target for current psychotherapies. Building on our recent development of comparative gene editing, we here present an adeno-associated virus-mediated CRISPR/Cas9 strategy to reduce in vivo dopamine receptors D1 and D2 levels across the rodent phylogeny. Using this approach, we achieved specific reduction of receptor levels in three rodent species (house mouse, prairie vole, and Syrian hamster), which we demonstrate with radioactive ligand binding assays. This toolkit expands the reach of comparative gene editing approaches, enabling functional investigation of the dopaminergic system across rodent species. Thereby, it supports comparative neuroscience by facilitating the identification of conserved versus species-specific neural mechanisms with enhanced translational potential.

ABSTRACT Long-read sequencing can characterize complex genome editing-induced DNA sequence changes such as large deletions, insertions, and inversions that are difficult to detect using short-read sequencing. However, PCR amplification and sequencing errors complicate accurate variant detection, and existing analysis tools are not optimized for gene editing specific allelic outcomes. Here we present CRISPRLungo, a computational pipeline specifically designed for long-read amplicon sequencing of gene edited samples. CRISPRLungo incorporates unique molecular identifier (UMI)-based error correction and statistical filtering to distinguish true editing events from background noise, enabling robust detection of small indels and structural variants. Through systematic benchmarking using simulated datasets, we demonstrate that CRISPRLungo outperforms existing approaches in both accuracy and read recovery. CRISPRLungo supports both Oxford Nanopore and PacBio platforms and identify previously undetected structural variant edits such as inversions in published CRISPR datasets. To demonstrate allele-specific edit quantification, we applied CRISPRLungo to analyze edited primary cells from a patient with harboring compound heterozygous SBDS mutations, accurately quantifying SBDS editing outcomes despite contaminating reads from the homologous SBDSP1 pseudogene. To maximize accessibility, we developed a fully client-side web application requiring no installation, making advanced long-read analysis accessible to researchers regardless of computational expertise. CRISPRLungo is freely available at https://github.com/pinellolab/CRISPRLungo with a user-friendly web interface available at https://pinellolab.github.io/CRISPRLungo .

Gene editing using CRISPR/Cas9 in vivo offers a powerful tool to investigate pain mechanisms. We validated the use of conditional knock-in mouse model expressing Streptococcus pyogenes CRISPR associated protein 9 selectively in sensory neurons by crossing with Scn10a -Cre driver. Transgene expression was confirmed in key tissues including the dorsal root ganglia (DRG) and sciatic nerve. To assess in vivo editing efficacy, RNA guides targeting GFP or TRPV1 were intrathecally administered. A dose of 3 µg RNA guides significantly reduced GFP expression, and two rounds of nanoparticle delivery targeting TRPV1 resulted in ∼65% reduction in DRG and ∼55% in sciatic nerve without triggering caspase-3-mediated apoptosis or motor deficits. Edited animals exhibited increased withdrawal latencies to heat and reduced nocifensive behaviors following capsaicin injection. Their responses to capsaicin-evoked thermal hyperalgesia and mechanical allodynia were diminished. This approach enables rapid and efficient sensory neuron-specific CRISPR/Cas9 gene perturbations for pain research in mice. We envisage that this method can be employed both for the exploration of molecular mechanisms underlying nociception and for the validation of therapeutic targets associated with pain.

New viral approaches have revolutionized neuroscience by precisely delivering genes in neurons; for example, to control or monitor activity in specific neuronal cell types. In contrast, the manipulation of oligodendrocytes requires the Cre-LoxP system and gene-by-gene engineering, breeding, and genotyping. Here we introduce OASIS ( O ligodendrocyte A AV-CRISPR mediated S pecific In vivo editing S ystem), a versatile platform that combines SELECTIV, an AAV-receptor-based transduction strategy, with HiUGE, an NHEJ-mediated CRISPR/Cas9 knock-in approach. We show efficient and specific oligodendrocyte transduction across the brain and tagging of endogenous cytoskeletal, myelin, cell adhesion, scaffolding, and junctional proteins. OASIS enables sparse yet reliable labeling, allowing direct visualization of a protein’s subcellular localization with single-cell resolution. We successfully fused the biotin-ligase TurboID with endogenous oligodendroglial Neurofascin-155, thereby achieving targeted biotinylation of the axoglial junction. OASIS is rapidly customizable for any gene-of-interest. Together, OASIS overcomes longstanding barriers in oligodendrocyte biology, providing a powerful system for precise, customizable genome editing and subcellular visualization in the adult brain.

In hematology/oncology clinics, molecular diagnostics based on nucleic acid sequencing or hybridization are routinely employed to detect malignancy-associated genetic mutations and are instrumental in therapeutic stratification and prognostication. However, their limited cost-efficiency constrains their use in pre-malignant screening—specifically, the detection of rare circulating mutant blood cells in asymptomatic individuals. In both neonates and adults, the presence of malignancy-associated mutations in peripheral blood correlates with an elevated risk of future neoplastic transformation, with certain mutations, such as KMT2A rearrangements, exhibiting near-complete penetrance. If feasible, pre-malignant screening could enable early intervention and even disease prevention. Here, we introduce a high-throughput, single-cell computer vision platform capable of identifying mutant peripheral blood cells by recognizing mutation-specific morphological features. The morphology recognition module was developed through cross-species learning from murine to human datasets, enabling a generalizable and cost-effective approach for detecting mutations in live blood cells. The platform holds promise for translation into pre-malignant screening applications in asymptomatic neonates and adults as well as measurable residual disease monitoring in malignancies. Furthermore, it provides a novel single-cell morphological data modality that complements existing molecular layers, including genomics, epigenomics, transcriptomics, and proteomics.

Complex microbial phenotypes involve the combined activity of diverse gene regulatory networks. However, the majority of reverse genetics approaches in microbial pathogenesis research have focused on single-gene perturbation studies, in part due to the lack of available genetic tools in many pathogens. Developing enhanced versions of CRISPR-Cas platforms holds significant promise for improving the scalability of microbial functional genomics research. Here, we demonstrate highly efficient, inducible, and multiplexed activation and repression in the major human fungal pathogen Candida albicans by translating the hyperdCas12a variant to the fungal kingdom. This represents the first application of a CRISPR-Cas12 system in a human fungal pathogen. We profile the effectiveness of our new CRISPRa and CRISPRi tools and achieve tunable levels of target modulation. Further, we demonstrate that perturbing combinations of genes in the drug efflux and ergosterol biosynthesis pathways reveals important redundancies and synergistic properties in drug resistance circuitry. Our hyperdCas12a platform is thus an efficient system for the rapid generation of combinatorial mutants that will enable the mechanistic understanding of genetic interactions involved in diverse phenotypes in C. albicans . The enhanced activity with hyperdCas12a in fungi suggests it could be translated to other microbes as a powerful tool for studying genetic interactions.

SUMMARY Peripheral differentiation of regulatory T cells (pTregs) promoted by foreign antigens encountered in barrier tissues is considered a unique contributor to immunological tolerance to obligate non-self, like food or symbiotic microbes. The relative importance of adaptive recognition via the T cell receptor (TCR) vs environmental small-molecule or neuroimmune cues, is poorly understood. We leverage CRISPR-based TCR editing to perform in primary T cells in vivo , with a large panel of TCRs, a screen to assess pTreg differentiation induced by self, microbial, or dietary antigens. All antigen classes drive pTreg differentiation, which varies with the origin of the TCR: TCRs derived from Tregs enable pTreg differentiation much more effectively than those from Tconv. TCRs recognizing self, microbial, or dietary antigens elicit distinct pTreg phenotypes, Helios⁺, RORγ⁺, or both. Mechanistically, these trace to different types of antigen-presenting-cell involved. That Treg-derived TCRs preferentially drive tolerogenic fate speaks to preferential drivers of tolerogenic therapy.

Background: Aging brains are shaped by a persistent dialogue between declining neurogenesis and rising neuroinflammation. Neural stem cells progressively lose regenerative capacity, while microglia and astrocytes shift toward maladaptive states that erode synaptic plasticity and cognition. This convergence defines inflammaging, a slow yet relentless process that undermines resilience. However, the field remains hampered by critical gaps: incomplete mapping of microglial heterogeneity, poorly understood epigenetic scars from inflammasome signaling, lack of longitudinal data, unclear niche-specific immune mechanisms, and uncertain cross-species relevance. This review addresses these pressing barriers, aiming to transform fragmented insights into actionable strategies. Summary: I chart how neurogenesis and neuroinflammation operate in continuous dialogue, identify five major knowledge gaps, and evaluate strategies to reprogram this interaction. Approaches include longitudinal imaging, niche-focused immunomodulation, glial subtype reprogramming, brain-penetrant inflammasome inhibitors, and CRISPR-based epigenetic editing. Each strategy is mapped against translational potential, short-term feasibility, and long-term vision, with emphasis on how mechanistic precision can guide clinical innovation. Conclusion: Here I highlight that neurogenic potential is not entirely lost with age but may be preserved or restored by tuning immune and epigenetic environments. This review proposes a roadmap for reshaping the aging brain’s fate, offering mechanistically grounded strategies to delay cognitive decline. Beyond neurology, the work underscores a broader principle: by integrating cellular plasticity with immune modulation, science edges closer to re-engineering resilience across the lifespan.

ABSTRACT Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPF’s contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrate’s rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.

Abstract Orofacial clefts represent the most prevalent congenital anomalies affecting the craniofacial region. They can be evoked by a disturbed development of either oral epithelium or cranial neural crest-derived mesenchyme, or by disruptions of their interplay. IRF6 is a well-known risk gene associated with orofacial clefts. Its expression in the oral epithelium depends on the transcription factor AP-2α, encoded by TFAP2A. We here show by immunofluorescence on mouse embryonic sections and by mining of single cell RNA-seq data that IRF6 is also expressed in cranial neural crest-derived tissue in mice and humans, together with TFAP2A and SOX9. The IRF6 enhancer MCS-9.7 can be activated by the transcription factor SOX9, mutations of which cause Pierre Robin sequence, a craniofacial anomaly that includes cleft palate. This SOX9-dependent activation is influenced by the single nucleotide variant rs76145088 that is associated with orofacial clefting. Inactivation of Sox9 in a murine neural crest cell line by CRISPR/Cas9 results in loss of Irf6 expression. We conclude that dysregulation of the SOX9–IRF6 axis in cranial neural crest cells could be relevant for the pathogenesis of orofacial clefting.