Cell Reports Methods

Human midbrain organoids (hMBOs) are emerging in vitro models to mirror the cellular diversity and the structural complexity of the developing human brain. However, the dense neural network, limits the investigation of individual cells morphology or cell-cell connectivity, which is mostly restricted to fixed organoids following extensive optical clearing techniques. To better resolve individual cells within a brain organoid and for longitudinal tracking of its growth and development, we turned to adeno-associated virus (AAVs) for targeted gene delivery. In particular, we applied AAVs for expressing specific markers that provide the foundation to image individual cells within 3D hMBOs. Thus, we developed a phenotypic platform to specifically inspect the neuronal and astrocytic cytoarchitecture and to examine their connectivity in living hMBOs derived from two genetically unrelated control iPSC lines. We demonstrate that through AAV transduction, we could capture and reconstruct the 3D architecture of both neurons and astrocytes within the hMBO as a whole. Transduced cells exhibited an intrinsic heterogeneity in term of soma volume, arbor complexity and territory covered, regardless of both genetic background, age, and cell-type. Yet, these cellular morphometrics remained equivalent between the two cell lines, indicative of homogeneity in hMBO cellular development. We were able to establish longitudinal profiling of transduced cells, demonstrating how neurons and astrocytes could expand their network over time. Lastly, we describe time-lapse studies to track cellular motility and morphology fluctuations in neurons and astrocytes over time, highlighting the dynamic nature of these cells within the ramified architecture of the neural network in the developing hMBOs. Overall, our platform underscores the versatility of AAVs in studying single cell-morphometrics and cellular connectivity for longitudinal monitoring of cellular dynamics in live 3D hMBOs instead of a static snapshot.

Double-stranded RNA (dsRNA) is recognized by cellular receptors as a sign of viral infection, triggering the innate immune response. Increasing evidence shows that cellular dysregulation, for example in immune disorders and neurodegenerative diseases, can also lead to accumulation of endogenously produced dsRNA that stimulates a viral-like immune response. Additionally, dsRNA contamination in RNA therapeutics can lead to harmful side effects via a similar pathway. Despite the clinical relevance of dsRNA, reliable tools for its detection remain limited. At present, dsRNA detection relies almost exclusively on the monoclonal antibodies J2 and K1, which suffer from sequence bias and low sensitivity, limiting their reliability. To address this challenge, we aimed to repurpose naturally occurring dsRNA-binding domains (dsRBDs) to produce reliable, pan-specific affinity reagents for dsRNA. We first systematically screened the dsRBDs of the three human adenosine deaminases acting on RNA (ADARs). This analysis identified ADAR3 dsRBDs as promising candidates due to their reduced sequence dependence compared to the dsRBDs of ADAR1 and ADAR2. We then engineered ADAR3-derived dsRBD constructs having varying linker lengths and domain combinations, allowing us to specifically vary the length cutoff of dsRNA detected, thus creating dsRNA accumulation detected by ADAR3 RBDs (dsRADAR) affinity reagents. Finally, we demonstrate the superior performance of dsRADAR over currently available dsRNA antibodies in a cell model of viral infection and a tissue model of gastric inflammation. Together, dsRADAR provides a sensitive and reliable approach for imaging and quantifying diverse dsRNA structures in a variety of biological contexts. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/724404v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d89c30org.highwire.dtl.DTLVardef@1f64fc1org.highwire.dtl.DTLVardef@1ee391forg.highwire.dtl.DTLVardef@e834a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

Basal forebrain cholinergic neurons project widely to the cerebral cortex and participate in cerebrovascular regulation. Although cholinergic axons are distributed around the cerebrovasculature, their functional relationship with arteriolar dynamics remains unclear. In this study, we established an in vivo two-photon imaging approach to simultaneously measure Ca2+ signals in cholinergic axonal varicosities and arteriolar diameters in urethane-anesthetized mice. An adeno-associated virus (AAV) vector (rAAV-ChAT-jGCaMP8s) was injected into the nucleus basalis of Meynert. In vivo imaging of the frontal cortex revealed bead-shaped GCaMP signals around the arterioles. Pinch stimulation transiently increased Ca2+ signals in periarteriolar varicosities, followed by arteriolar dilation, with an approximately 2-s delay between their peaks. Linear regression analysis disclosed a significant relationship between the magnitudes of these changes. This approach enabled simultaneous evaluation of cholinergic axonal activity and arteriolar dynamics in vivo, providing a tool to investigate the cholinergic regulation of cerebrovasculature. HighlightsO_LIAAV-ChAT-GCaMP enables selective imaging of cholinergic projections C_LIO_LITwo-photon imaging reveals bead-shaped Ca2+ signals around arterioles C_LIO_LISensory stimulation increases periarteriolar cholinergic axonal Ca2+ signals C_LIO_LIAxonal Ca2+ signals are associated with arteriole dilation C_LI

Behavior arises from the complex interplay between an organisms nervous system, its genetic makeup, and the environment. High-resolution, high-throughput behavioral quantification is essential for dissecting biological function and the effects of genetic perturbation, but automated analysis remains challenging. Here, we present Autobehaver, an automated behavioral analysis pipeline based on a low-cost, high-throughput recording platform that captures videos of individual Drosophila. From each video, we extracted keypoints and used a custom Transformer to assign frame-wise behavior and orientation labels. We then converted these predictions into high-dimensional per-animal feature vectors and trained XGBoost ensembles to classify animals and identify the features that separated groups. By applying SHAP analysis to the classifier ensemble, we identified the behavioral features most informative for distinguishing groups of flies. We demonstrated the approach in several ways. First, we recovered known behavioral changes associated with heat-activated dTrpA1 activity in specific neural circuits. Second, we detected age-associated behavioral changes consistent with gradual impairment of locomotor and climbing ability. Finally, we used Autobehavers classifier ensemble to place animals with intermediate phenotypes along a behavioral axis and used feature-importance analysis to reveal the behavioral features underlying those intermediate states. Together, Autobehaver provides an interpretable framework for quantitative behavioral phenotyping and comparative analysis of complex genotypes.

Microglia represent the immune component of the central nervous system (CNS) that displays dynamic responses to injury and disease. Across the developing and mature CNS, microglia emerge as immunocompetent cells that continuously survey their surroundings to maintain tissue homeostasis and respond to threats. There remains a gap in 3D in vitro models that contain microglia and can provide both developmental and mature functional hallmarks. Using a 3D neural multicellular model, cortical microtissues, derived from primary rat cortical cells, we conducted live imaging to monitor microglia dynamics from early, middle, and late stage microtissue maturation. We optimized a within-micromold imaging approach that allows for live microglia imaging without removing microtissues from their culturing environment. We confirm that microglia exhibit baseline surveillance characterized by relatively stationary somas and highly dynamic cell processes that continuously extend and retract. Following proinflammatory challenges, microglia engulf lipopolysaccharide particles, accompanied by dynamic shifts in motility patterns; and rapidly respond to laser-induced tissue damage through process extension, whole-cell displacement, and local recruitment. Lastly, we show that microtissue age in culture strongly influences both baseline and directed motility profiles. Collectively, these studies demonstrate that within a 3D microenvironment, microglia exhibit pronounced changes in morphology, surveillance area, motility, and injury response across microtissue maturation. Microtissues can serve as a valuable in vitro platform for both microglia developmental studies and investigations of brain inflammation related to CNS injuries, infections, and diseases.

Oligodendrocyte-enriched cortical organoids (OCOs) are a powerful platform for modeling oligodendrogenesis in a human cellular context. However, neuronal activity is impaired in conventional culture media, limiting assessment of neuronal function in conjunction with oligodendrocyte biology. To address this, we used a modified BrainPhys medium termed neuronal activity medium (NAM) and defined the optimal developmental window for NAM exposure to generate OCOs with robust neuronal activity (NAM-OCOs). Stage-specific exposure to NAM, prior to oligodendrocyte expansion, leads to enhanced structural maturation, as evidenced by increased organoid size, heightened synaptogenesis, and upregulation of transcripts associated with neuronal complexity. Further, NAM-OCOs display increased cellular heterogeneity, including greater representation of GABAergic interneurons while preserving oligodendrocyte development and maturation. Altogether, our studies demonstrate that stage-specific exposure to an activity-permissive environment enhances neuronal activity, establishing an OCO model which integrates neuronal activity with oligodendrocyte development and maturation. HighlightsO_LIIncreased neuronal activity in oligodendrocyte-enriched cortical organoids (OCOs) C_LIO_LIStage-specific Neuronal Activity Medium (NAM) optimizes activity C_LIO_LINAM-OCOs display increased cellular heterogeneity and neuronal maturation C_LIO_LIOligodendrogenesis is preserved in NAM-OCOs C_LI eTOC blurbIn this article, Chung et al enhance neuronal activity in oligodendrocyte-enriched cortical organoids (OCOs) through stage-specific exposure to Neuronal Activity Medium (NAM). OCOs exposed to NAM display elevated cellular heterogeneity, structural maturation, and synaptogenesis, while preserving oligodendrocyte development and maturation. These results establish an increasingly comprehensive OCO model for studying neuronal function and oligodendrogenesis.

Single-cell RNA-sequencing-based characterization of cells that belong to the neoplastic clone is a major challenge in hematologic neoplasms, where malignant and normal cells coexist. Confident molecular profiling requires simultaneous analysis of gene expression and genetic mutations in individual cells, an ability that is not supported by the standard 10X Genomics workflow. Here, we developed a post-hoc targeted genotyping method for samples processed with the 10X Genomics 3 workflow. To establish the approach, we mixed two types of leukemic cells harboring distinct mutations and subjected them to single-cell RNA-sequencing. Repurposing an intermediate product of the experimental process allowed us to enrich for transcripts containing mutation sites. Long-read PacBio sequencing genotyped the transcripts and captured the associated cellular and molecular barcodes, allowing us to bioinformatically integrate the mutation and transcriptomic data at single-cell resolution. Our method demonstrates the detection of mast cell leukemia-associated point mutations in the KIT gene and chronic myeloid leukemia-associated BCR::ABL1 fusion transcripts. Single-cell analysis of primary leukocytes from chronic myeloid leukemia detected mutated cells at diagnosis, but not during imatinib treatment. Taken together, the method constitutes a broadly applicable framework for post-hoc genotyping of cells analyzed with single-cell RNA-sequencing.

Targeted protein degradation using conditional degron tag (CDT) technology is a powerful method for rapidly degrading a protein of interest (POI) upon the addition of a degrader drug. A prerequisite for the temporally controlled degradation of an endogenous POI is the generation of homozygous knock-in cells with the degron tag integrated at either the N- or C-terminus of their gene loci. However, obtaining those homozygous knock-in cells often requires selecting many single-cell clones, as human cells typically exhibit low homology-directed repair (HDR) activities. Additionally, tagging a degron to an endogenous protein may inadvertently reduce protein expression, potentially affecting protein function even before the drug is administered. Here, we develop a method for generating degron-tagged knock-in cells that allows us to skip the laborious single-cell cloning. This method arose from our observation that most knock-in cells carry the degron tag only in one allele (heterozygous), while the other allele typically harbors a frameshift insertion/deletion. This observation allowed us to bypass the need for single-cell cloning. We validated our method by knocking in degron tags at the N-terminus of cytoplasmic dynein1 subunits or Adaptor Protein 2 (AP2) subunit. Our experiments confirmed the rapid degradation of these proteins and their functional inhibition in bulk cell populations. Additionally, to mitigate the reduced expression often associated with the degron tagging, we established a method to control expression levels by inserting a mini-promoter immediately upstream of the knock-in cassette. Our method simplifies the workflow for degron tag knock-ins and enhances the versatility of these valuable technologies.

Dual-organism RNA sequencing (RNA-seq) experiments, in which the transcriptomes of a host and a microbe are sequenced simultaneously, are increasingly used to study plant-microbe interactions. A central analytical goal is identifying effector proteins and their host targets through gene co-expression. Weighted Gene Co-expression Network Analysis (WGCNA) is the dominant tool for gene co-expression analyses, yet its ability to recover interaction-interface genes from a merged dual-organism matrix has not been systematically characterised. Here we present a simulation framework using real gene models from Hordeum vulgare (barley) and Blumeria graminis f. sp. Hordei M.Liu & Hambl (powdery mildew) to evaluate single-network WGCNA across a gradient of plant-to-fungal library size ratios (1:1-20:1), three levels of co-expression signal strength, and three WGCNA network construction types (signed, unsigned, signed hybrid). We embed 20 model effector genes (bridge genes) driven by a mixed host-pathogen eigengene and evaluate recovery using four metrics aligned with the biological objective: cross-species hub rank, top-decile hub enrichment, bridge gene detection rate, and bridge co-separation (the fraction of effector-target pairs co-assigned to the same detected module). Across 225 simulation runs (15 conditions x 5 replicates x 3 network types), bridge genes are robustly identifiable as cross-species connectivity hubs (mean rank 0.92 versus 0.50 for module genes) but co-assignment of effector-target pairs to the same module fails in 41% of runs due to scale-free topology collapse. Signal strength (2 = 0.12) and library ratio (2 = 0.22) are the primary determinants of co-separation, while network type choice accounts for less than 2%. A read-depth bias systematically inflates pathogen gene hub ranks relative to host genes at high ratios. These results establish that the method can identify effector candidates as cross-species hubs under a broad range of conditions, but reliable co-assignment requires adequate pathogen read depth and strong co-expression signal--properties that experimental design, not analytical parameterisation, must provide.

The tissue-resident immune system involves complex 3D assemblies that interact with extended structures such as blood vessels and nerves. These interactions are difficult to study using conventional 2D profiling because they span many tissue sections. In animal tissues, volumetric imaging approaches such as light-sheet fluorescence microscopy (LSFM) are widely used to study 3D tissue organization, with labelling often aided by genetically encoded reporters and vascular dyes. In contrast, LSFM of human specimens remains underdeveloped because most clinical samples are available only as formalin-fixed paraffin-embedded (FFPE) tissue, limiting labeling strategies primarily to dyes and antibodies. Here, we present a volumetric cyclic immunofluorescence (v-CyCIF) and virtual H&E toolbox that overcomes key barriers to multiplexed imaging of immune cells and nerves in human specimens up to 1 mm thick. We use v-CyCIF to study neuroimmune interactions in normal and cancer tissues and to immunoprofile intact secondary and tertiary lymphoid structures. Re-embedding and sectioning of specimens following volumetric imaging enables high-plex high-resolution analysis of subcellular structures and cell-cell interactions associated with immune cell activity. v-CyCIF therefore provides a flexible framework for multi-scale 3D profiling of clinical specimens across imaging formats and resolutions.

During forebrain development, inhibitory interneurons and oligodendrocyte progenitor cells migrate long distances into the developing dorsal cortex. Human induced pluripotent stem cell-derived forebrain assembloids (FAs) provide direct experimental access to this migratory process in vitro. Using viral labeling to express yellow fluorescent protein (EYFP) and tandem-dimer tomato (tdTomato) driven by EF1 or SOX10 promoters, respectively, we tracked cells in FAs over 15-17h using spinning disk confocal microscopy. We developed an end-to-end processing pipeline for 4D volumetric imaging data, consisting of background subtraction and drift correction, manual cell coordinate tracking, and an analysis workflow to describe migratory cell behavior. Image preprocessing significantly improved data quality for subsequent manual tracking in datasets with heterogeneous labeling density and brightness. Trajectory analysis of 336 EYFP- and 337 tdTomato-labeled cells from twelve FAs indicates that most cells show super-diffusive directed motility. Our pipeline represents a key resource for cell tracking in FAs and similar three-dimensional platforms. This pipeline represents the first open tracking resource for iPSC-derived FAs and can be used as a ground-truth resource for the development of automated cell detection and tracking algorithms.

Lentiviral vectors are commonly used to introduce chimeric antigen receptor transgenes into T cells, but routine assays quantify vector copy number or integration sites without sequencing full-length integrated vectors. HIV-1 proviruses often acquire large deletions and cytidine deaminase-driven hypermutation; whether similar variation occurs in therapeutic lentiviral vectors is unclear. We adapted a novel long-read capture approach to enrich long fragments spanning vector DNA and adjacent human sequence, enabling simultaneous integration-site mapping and proviral integrity analysis with single-molecule resolution. In research-grade CAR T cells produced with an experimental, transient-transfection lentiviral vector workflow, 40% of integrated vectors carried recurrent deletions that removed the internal promoter or parts of the chimeric antigen receptor cassette. The dominant promoter deletion was present in the viral stock. In clinical chimeric antigen receptor T cell products, promoter deletions were less frequent, but detectable pre-infusion and post-infusion. Across datasets we observed widespread G-to-A substitutions consistent with restriction factor editing, including changes predicted to introduce premature stop codons within the transgene open reading frame. Our method reveals proviral variants invisible to standard quality-control assays and provides a framework to improve vector production and monitor transgene integrity in clinical products.

CaMKII promoter is widely used to label and manipulate hippocampal pyramidal neurons via transgenic mouse lines or viral approaches. While it targets most excitatory neurons, a small subset remains unlabeled and often overlooked. We present an AAV-based strategy combined with CaMKII-driven Cre expression to access and study this remaining population. Furthermore, we provide a detailed protocol for in-house AAV production, targeted stereotaxic delivery, and functional validation of targeted neurons through slice electrophysiology and behavior. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/723440v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@3a31ccorg.highwire.dtl.DTLVardef@9b7e90org.highwire.dtl.DTLVardef@92297borg.highwire.dtl.DTLVardef@1e159eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

Advances in transcriptome profiling have revealed transcriptomic differences across different cellular states. However, functional interpretation requires precise perturbation tools and experimental frameworks. This study benchmarked two widely used modalities: CRISPR interference (CRISPRi) and Cas13d/CasRx. A standardized workflow was established to generate human pluripotent stem cells (PSCs) with inducible ZIM3-dCas9 or CasRx expression. The cell lines were subjected to flow cytometry, copy number, and immunocytochemical analyses. The knockdown performance was validated via robust OCT4 suppression and the expected downstream effects on pluripotency genes. Time-course measurements indicated that CRISPRi produced faster and stronger repression but slower recovery after inducer withdrawal. In contrast, CasRx yielded slower and typically weaker knockdown with rapid reversibility. Furthermore, a key limitation of CRISPRi was demonstrated using the ATF5-NUP62 locus, wherein CRISPRi could co-repress genes with overlapping promoter regions. In contrast, CasRx avoids these limitations and supports isoform-resolved targeting of circular and alternatively spliced transcripts, albeit with variable efficiency. These results provide practical guidance for selecting complementary knockdown tools to improve the interpretability of transcriptomic function studies. MOTIVATIONAdvances in transcriptome profiling have enabled the detection of subtle cell type-specific differences. However, mechanistic interpretation still depends on perturbation tools that can modulate transcripts with high precision and efficiency. Recent CRISPR-based modalities, CRISPRi and Cas13/CasRx, function as robust and orthogonal methods to achieve the knockdown of specific gene targets. However, a standardized approach for cell line preparation and comparative studies on their relative performances and limitations remains unclear. Consequently, this study presents a standardized workflow for generating cell lines that support high-efficiency knockdown using CRISPRi and CasRx. Moreover, it compares the trade-offs in potency, reversibility, and isoform resolution, along with a practical overview of method-specific pitfalls to guide tool selection and data interpretation in future studies. HIGHLIGHTSO_LIDoxycycline-inducible AAVS1 knock-in human PSC platforms for CRISPRi (ZIM3-dCas9) and CasRx (RfxCas13d) were generated to enable standardized RNA perturbation experiments. C_LIO_LIThe prepared cell lines demonstrated strong OCT4 knockdown, with expected downstream effects on the expression of another pluripotency gene, NANOG. C_LIO_LIA comparison of knockdown characteristics and their reversibility revealed rapid and sustained repression with CRISPRi, whereas slow but rapid recovery was observed with CasRx. C_LIO_LIA CRISPRi-specific off-target effect arising from TSS proximity/overlap (ATF5-NUP62) was identified, whereas CasRx achieved ATF5 knockdown without collateral repression of the neighboring NUP62 gene. C_LIO_LICasRx enables isoform-resolved knockdown of structural isoforms (circHIPK3 vs. linear HIPK3 mRNA) and splice isoforms (RAB6A-iso1 vs. RAB6A-iso2). C_LI

Cryopreservation offers an option for long-term storage and global distribution of complex in vitro models, yet protocols for multicellular microphysiolgocial systems (MPS) such as brain organoids/spheroids remain limited. Here, we systematically compared three commercially available cryopreservation (mFreSR, CryoStorCS10, and 3dGRO) and two freezing time points, and established a robust workflow for freezing and recovering brain organoids. After defrosting, we assessed morphology and metabolic activity. We also evaluated electrophysiology, calcium transients, and neurite outgrowth. In addition, we measured astrocyte migration, apoptosis, mitochondrial integrity, microglia survival, and neural marker expression. We found that organoids require a 4-week recovery period to regain structural and functional stability. Although organoids frozen at week 6 showed higher metabolic activity after recovery, organoids cryopreserved at week 2 had clearly better functional outcomes. They exhibited stronger spontaneous network firing and maintained calcium transients. Finally, incorporated microglia-like cells survived the freezing and displayed comparable morphology to unfrozen controls. Across the endpoints measured here, 3dGRO showed the most favorable overall performance; formal ranking across media awaits harmonized normalization, single-organoid electrophysiology, and prespecified QC thresholds. Together, these results define a practical and reproducible cryopreservation strategy that preserves key physiological features of brain organoids and supports the establishment of ready-to-use organoid banks. The ability to reliably store and distribute complex brain-like tissues represents an essential step toward global standardization, scalable experimentation, and wider adoption of human-relevant microphysiological systems. Together, these results demonstrate recovery of key physiological features in the subset of organoids that remain viable after thaw and support the feasibility of brain organoid banking.

Transgenic mouse models are indispensable for dissecting disease mechanisms; yet, their interpretability is frequently compromised by cryptic genomic alterations introduced during transgenesis. Thus, robust quality control strategies are needed to elucidate integration architecture and evaluate model performance when such unintended events occur. Here, we applied unbiased whole-genome long-read sequencing using the PacBio Revio to investigate a mouse model exhibiting unexpected transgene silencing, originally designed to recapitulate autosomal-dominant hereditary macular dystrophy driven by upregulation of a ZZEF1-ALOX15 fusion gene. Long-read sequencing analysis revealed a [≥]29-kb head-to-tail concatemer containing more than three copies of the transgene vector. Reconstruction of transgene-genome junctions revealed off-target integration of the concatemer into the calcium-sensing receptor gene (Casr), along with exogenous E. coli DNA, that together defined final transgene architecture. 5-methylcytosine profiling identified hypermethylation of the transgene promoter and additional phenotyping indicated disruption of endogenous Casr function resulting from the rearrangement. Our workflow enabled direct detection of transgene concatenation and off-target mapping. These findings establish long-read sequencing as a powerful and scalable quality control standard for genetically engineered animal models, uniquely capable of uncovering hidden genomic complexity, resolving aberrant phenotypes, and enhancing the reliability of in vivo disease modelling.

Connecting protein post-translational modifications (PTMs) to phenotypic outcomes is a central challenge. Although phosphoproteomics has richly catalogued specific sites, reliable methods to measure the endogenous effects of individual phosphosites on cellular fitness and signaling are still lacking. Here, we introduce CRISPR-PTM and CRISPR-VEIS as complementary platforms for quantitative, endogenous phosphosite interrogation at both individual and clustered phosphorylation events. CRISPR-PTM is a multiplexed knock-in framework generating defined phosphosite variants with internal allelic markers, enabling precise relative fitness effects in pooled populations. CRISPR-VEIS (Visualisation of Edits In Situ) is an in situ mRNA-genotyping approach that directly links endogenous allelic edits to single-cell phenotypes, addressing needs for subclonal isolation or exogenous reporters. We applied these methods to the WEE1-CDK1 regulatory pathway, where canonical CDK1-Y15 phosphorylation alone cannot explain WEE1 loss or inhibition phenotypes. CRISPR-PTM systematically quantified fitness consequences of CDK1 phosphosite variants and identified Y19 as a previously unrecognized WEE1-dependent inhibitory site. Single non-phosphorylatable substitutions at Y15 or Y19 had minimal impact, but combined CDK1-Y15F/Y19F editing caused pronounced fitness defects, phenocopying WEE1 inactivation and showing epistasis to WEE1 inhibitors. CRISPR-VEIS further demonstrated that acute endogenous editing of both sites correlated with elevated CDK activity at the single-cell level. Together, CRISPR-PTM and CRISPR-VEIS provide broadly applicable approaches for quantitative analysis of PTM function, enabling direct linkage of endogenous phosphosite variation to cellular fitness and signaling phenotypes.

Long-term, automated tracking of group-housed social animals using RFID (radio frequency identification) is a promising approach in ethological neuroscience. However, low-frequency (LF) RFID, while long-established in the field, is constrained by its inherent low data rates, which lead to two critical limitations: (1) compromised spatiotemporal resolution, and (2) the inability to identify multiple tags (animals) simultaneously. To address these limitations, we developed eeeHive, a high-frequency (HF) RFID-based animal tracking system with a fully custom hardware architecture that enables high-speed, multiplexed antenna polling and concurrent multi-tag reading. The polling time per antenna in eeeHive was 5.9 ms, with an additional 8.2 ms read time per tag. We applied the system to track 24 mice for one week, and six common marmosets for seven weeks. The system successfully tracked individuals even within dense clusters, revealing complex behavioral traits characterized by spatial utilization, temporal dynamics, behavioral regularity, and inter-individual relationships. Additional tests with Japanese fire-bellied newts and Nile tilapia juveniles demonstrated comparable tracking performance in aquatic environments. Taken together, eeeHive overcomes the inherent limitations of conventional LF RFID, establishing a powerful HF RFID-based platform for fine-scale behavioral tracking of group-housed animals across terrestrial and aquatic species.

The binding of transmembrane (TM) ligands to their cognate TM receptors on neighboring cells governs intercellular adhesion and direct cell-cell communication. However, these interactions are difficult to study in vitro because they depend on membrane presentation, ligand orientation, receptor clustering, and avidity, features often not captured by soluble recombinant ligands or cell-free assays. Here, we describe a flow cytometry-based assay using fluorescent, lentiviral-derived virus-like particles (VLPs) displaying TM ligands to quantify binding to their receptors on target cells. Fluorescent VLPs are generated in-house by plasmid transfection in HEK293T cells and enable direct fluorescent detection without fluorochrome-conjugated secondary antibodies. The system is modular and readily accommodates engineered ligand constructs, including patient-derived variants. We applied this platform to generate ICAM-1-displaying fluorescent VLPs and to study human LFA-1 function in patient-derived leukocytes. This protocol provides a detailed workflow for VLP production and in vitro binding assays, offering a simple, quantitative, and cost-effective approach for studying TM ligand-receptor interactions in a membrane context. The system is well suited for mechanistic studies, functional assessment of patient-derived variants, and direct binding assays using patient-derived cells. Integrating the assay into multicolor flow cytometry panels enables simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. Key featuresO_LIQuantifies TM ligand-receptor binding in a membrane context using fluorescent VLPs and flow cytometry. C_LIO_LIFully in-house, modular system based on plasmid transfection in HEK293T cells, without reliance on recombinant ligands or fluorochrome-conjugated secondary antibodies. C_LIO_LISupports testing of engineered ligand variants, including patient-derived alleles, and direct functional studies on patient-derived cells. C_LIO_LICompatible with multicolor flow cytometry panels, enabling simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. C_LI Graphical overview O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/725198v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@a43069org.highwire.dtl.DTLVardef@166491borg.highwire.dtl.DTLVardef@49c7d4org.highwire.dtl.DTLVardef@1de36a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Among mammals, spiny mice (Acomys spp.) exhibit the unique capacity to regenerate parts of their nervous system. Studying this phenomenon has the potential to reveal new targets that can slow or halt human neurodegenerative disorders. Unfortunately, research tools (e.g., transgenic lines, gene delivery vehicles) are lacking compared to those available for other rodent models. Here, we tested systemic adeno-associated viral vectors (AAVs) in Acomys dimidiatus and identified three promising candidates: X1.1, CAP-Mac, and MaCPNS1. Characterizing their tropism following intravenous delivery, we found that in the brain, MaCPNS1 and X1.1 primarily transduced astrocytes. In the peripheral nervous system, MaCPNS1 efficiently transduced dorsal root ganglia, axon bundles of the ear pinnae, and enteric neurons throughout the gastrointestinal tract. As a proof-of-concept, we used MaCPNS1 to chemogenetically modulate the activity of enteric neurons, successfully decreasing gastric motility in vivo and increasing colonic motility ex vivo. We expect these findings to enable functional studies of the uniquely regenerative nervous system of Acomys, which may in turn help advance neuroregenerative therapeutics for humans. Summary StatementIdentification of an AAV tool to efficiently deliver transgenes to the central and peripheral nervous systems of spiny mice enables functional studies of the nervous system in a mammalian model of regeneration.