In this study, we demonstrate the potential of cerebellar organoids for studying features of early human cerebellar development. Forkhead box protein P2 (FOXP2) is a transcription factor associated with speech and language development that is highly expressed in the developing brain. However, little attention has been directed to the study of FOXP2 in the early developing cerebellum. We used CRISPR gene editing in human iPSCs to generate a fluorescent FOXP2-reporter line. By combining transcriptomic analysis of iPSC-derived cerebellar organoids with published cerebellar datasets, we describe the expression and identify potential downstream targets of FOXP2 in the early developing human cerebellum. Our results highlight expression of FOXP2 in early human Purkinje cells and cerebellar nuclei neurons, and the vulnerability of these cell populations to neurodevelopmental disorders. Our study demonstrates the power of cerebellar organoids to model early human developmental processes and disorders.

Diatoms synthesize silica cell walls (frustules) with genetically encoded morphologies, ranging from nanopatterns to micropatterns, that far exceed current synthetic chemistry. Silaffins, a family of phosphoproteins undergoing complex post-translational modifications, have been isolated from frustules and shown to facilitate and regulate biosilica formation in vitro with long-chain polyamines. However, their particular role in frustule morphogenesis and functionality remains unclear. In this study, functions of two representative silaffins , TpSil1 and TpSil3 , were investigated in the model organism Thalassiosira pseudonana using gene overexpression and CRISPR/Cas9-mediated knockout approaches. Due to high sequence homology, TpSil2 was concurrently disrupted in TpSil1 knockout strains, while the homozygous knockout of TpSil3 proved to be lethal. Quantitative morphological analysis revealed distinct yet complementary roles: TpSil3 governs both microscale overall size and mesoscale features, including macropore (fultoportula) density and mesopore (cribrum pore) pattern, whereas TpSil1/2 exclusively contribute to macropore morphogenesis and mesopore density. Overexpression of silaffins increased silica deposition, while knockouts exhibited reduced silicification but enhanced cell growth and photosynthetic efficiency. Furthermore, these genetic modifications significantly influenced the physicochemical and optical properties of bulk frustules, potentially enhancing the hemostatic, catalytic and photonic performances, thereby positioning them as versatile candidates for a wide range of biotechnological and industrial applications. Collectively, our findings elucidate the distinct roles of TpSil1/2 and TpSil3 in diatom physiology and frustule morphology, highlighting a promising pathway for engineering nanostructured silica materials with tailored properties through synthetic biology.

3D genome organization is crucial to modulate gene expression. Topologically Associated Domains (TADs) isolate genes and their regulatory elements within the same topological neighborhood, avoiding crosstalk between regulatory elements. Perturbation of domain boundaries causes aberrant genomic contacts and gene expression misregulation. Architectural proteins such as CTCF and the cohesin complex are critical to form boundaries. However, we still lack a complete understanding of what makes a boundary more effective at insulating genomic contacts than others. To understand how domains are structured, we experimentally classified boundaries according to their chromatin accessibility as a proxy of protein occupancy in K562 human cells. We found that highly accessible boundaries are occupied by more proteins, are more robust contact insulators, have a more conserved CTCF DNA-binding motif and are more conserved across cell types in contrast to less accessible ones. By exploring the proteins enriched at boundaries with different accessibility, we found that CTCF and cohesin, together with REST, form a module, and ZFN316, together with EMSY, form another module, and both modules occupy boundaries very frequently. Finally, by using CRISPR-Cas9 mediated genetic edition of ZNF316 DNA-binding motif at a robust domain boundary, we demonstrate that ZNF316 can block chromatin contacts in the absence of CTCF. Our results emphasize the importance of protein combination and abundance to support boundary strength and propose ZNF316 as a novel architectural protein.

Streptomycetes hold immense potential for discovering novel bioactive molecules for applications in medicine or sustainable agriculture. However, high-throughput exploration is hampered by the current Streptomyces genetic engineering methods that involve the manual design of complex experimental molecular biological engineering strategies for each targeted gene. Here, we introduce StreptoCAD , an open-source software toolbox that automates and streamlines the design of genome engineering strategies in Streptomyces, supporting various CRISPR-based and gene overexpression methods. Once initiated, StreptoCAD designs all necessary DNA primers and CRISPR guide sequences, simulates plasmid assemblies (cloning) and the resulting modification of the genomic target(s), and further summarizes the information needed for laboratory implementation and documentation. StreptoCAD currently offers six design workflows, including the construction of overexpression libraries, base-editing, including multiplexed CRISPR-BEST plasmid generation, and genome engineering using CRISPR-Cas9, CRISPR-Cas3, and CRISPRi systems. In addition to automating the design process, StreptoCAD further secures compliance with the FAIR principles, ensuring reproducibility and ease of data management via standardized output files. To experimentally demonstrate the design process and output of StreptoCAD, we designed and constructed a series of gene overexpression strains in Streptomyces Gö40/10 , underscoring the tool’s efficiency and user-friendliness. This tool simplifies complex genetic engineering tasks and promotes collaboration through standardized workflows and design parameters. StreptoCAD is set to transform genome engineering in Streptomyces , making sophisticated genetic manipulations accessible for all and accelerating natural product discovery. Graphical abstract

Insect herbivores such as caterpillars, are under strong selection pressure from natural enemies, especially parasitoid wasps. Although the role of olfaction in host-plant seeking has been investigated in great detail in parasitoids and adult lepidopterans, the caterpillar olfactory system and its significance in tri-trophic interactions remain poorly understood. In this study, we investigated the olfactory system of Pieris brassicae caterpillars and the importance of olfactory information in the interactions among this herbivore, its host plant Brassica oleracea and its primary natural enemy Cotesia glomerata . To examine the role of olfaction, we utilized CRISPR/Cas9 to knockout the odorant receptor co-receptor ( Orco ). This knockout (KO) impaired olfactory detection and primary processing in the brain. Orco KO caterpillars exhibited reduced weight and lost preference for their optimal food plants. Interestingly, the KO caterpillars also experienced reduced weight when challenged by the parasitoid C. glomerata whose ovipositor had been removed, and the mortality of the KO caterpillars under the attack of unmanipulated parasitoids increased. We then investigated the behavior of P. brassicae caterpillars in response to volatiles from plants attacked by conspecific caterpillars and volatiles from plants on which the caterpillars were themselves attacked by C. glomerata . After analyzing the volatile compounds involved in these interactions, we concluded that olfactory information enables caterpillars to locate suitable food sources more efficiently as well as to select enemy-free spaces. Our results reveal the crucial role of olfaction in caterpillar feeding and natural-enemy avoidance, highlighting the significance of chemoreceptor genes in shaping ecological interactions.

ABSTRACT Resistance to endocrine therapy (ET) is common in estrogen receptor (ER) positive breast cancer. Multiple studies have demonstrated that upregulation of MAPK signaling pathways contributes to ET resistance. Herein we show that vandetanib treatment enhances sensitivity to ET in ET-sensitive and -resistant ER+ breast cancer models. Vandetanib treatment alters the gene expression program of ER+ breast cancer cells resulting in a less proliferative and more estrogen responsive Luminal-A like character. Tyrosine kinase network reprogramming was assessed using multiplexed kinase inhibitor beads-mass spectrometry (MIB/MS) assay to identify adaptive resistance mechanisms to vandetanib treatment, including upregulation of HER2 activity. Co-treatment to inhibit HER2 with lapatinib enhanced sensitivity to vandetanib, demonstrating biologic activity of HER2 upregulation. Using a CRISPR knockout model, we demonstrate that vandetanib effects are partially mediated by RET receptor tyrosine kinase. Finally, we use our operating room-to-laboratory assay that measures drug response in individual primary tumor cells in short term cultures to demonstrate conserved gene expression changes, including increased HER2 activity signatures, in vandetanib treated cells, and identify features associated with vandetanib response. These results support future investigation of RET targeting strategies considering reprogrammed networks, such as activated HER2, in patients with ET resistant ER+ breast cancer. SIGNIFICANCE Vandetanib enhances sensitivity to tamoxifen in ER+ breast cancer cells by reprograming kinase signaling networks, which can be used to select patients most likely to respond and develop more efficacious co-treatment strategies.

STXBP1 syndrome is a severe early-onset epileptic encephalopathy characterized by developmental delay and intellectual disability. This review addresses key challenges in STXBP1 syndrome research, focusing on advanced therapeutic approaches and experimental models. We explore gene therapy strategies, including CRISPR-Cas9, adeno-associated viral (AAV) vectors, and RNA therapies such as antisense oligonucleotides (ASOs), aimed at correcting STXBP1 genetic dysfunctions. The review presents in vivo and in vitro models, highlighting their contributions to understanding disease mechanisms. Additionally, we provide a detailed bioinformatic analysis of a Spanish cohort of 41 individuals with STXBP1-related disorders, offering insights into specific mutations and their biological implications. Clinical and translational perspectives are discussed, emphasizing the potential of personalized medicine approaches. Future research directions and key challenges are outlined, including the identification of STXBP1 interactors, unexplored molecular pathways, and the need for clinically useful biomarkers. This comprehensive review underscores the complexity of STXBP1-related infantile epileptic encephalopathy and opens new avenues for advancing understanding and treatment of this heterogeneous disease.

Non-pathogenic natural and recombinant strains of human Enteroviruses are the subject of ongoing study, with some strains having been approved for use as anticancer agents. The efficacy of on-colytic virotherapy is dependent upon the identification of the receptor utilized by a specific strain for cell entry and the presence of this receptor on the surface of cancer cells. Accordingly, a rapid and straightforward approach for determining the enteroviral receptors is necessary for the de-velopment of effective patient-specific virus-based cancer therapy. To this end, we created a panel of seven lines with double knockouts on the background of the HEK293T cell line, which lacks the IFNAR1 gene. In these lines, the main viral receptor genes, including PVR, CXADR, CD55, ITGA2, SCARB2, ICAM1, and FCGRT, were knocked out using the CRISPR/Cas9 system. A panel of lines was validated on a set of 12 Enteroviruses, providing a basis for studying the molecular mechanisms of enterovirus entry into cells and developing new therapeutic strains.

ABSTRACT Antimicrobial resistance (AMR) is an important threat to public health that has led to the development of innovative alternative treatments for bacterial infections, such as phage therapy. However, one of the greatest disadvantages of phage therapy is the generation of phage-resistant bacterial mutants via bacterial defence mechanisms, which are mainly contained in genomic islands (GIs) and controlled by the quorum sensing (QS) network. In this study, 309 pathogenic islands (PAIs) harbouring a total of 22.1 % of proteins related to anti-phage defence (APD) were detected in the genome of 48 K. pneumoniae strains. Several type I and type II CBASS systems were also detected in the genome of the 48 K. pneumoniae strains, but only 2 type II CBASS systems were located in PAIs. We constructed a knockout K. pneumoniae strain, not expressing the cyclase gene from the type II CBASS system present in PAIs, to study the regulatory role of QS in expressing the gene. As the anti-phage CBASS system is an abortive infection (Abi) system, the role of the type II CBASS system in regulating cell viability was assessed. The knockout strain was confirmed by targeting the LAMP-CRISPR-Cas13a technique specifically to the cyclase gene, and the same protocol was also used to detect the gene of the main cyclase in these type I CBASS systems, i.e. APECO1. The study findings demonstrate the regulatory role of the QS network in anti-phage defence systems. Finally, this is the first work which development an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 hours) in optimizing phage therapy by detecting bacterial resistance mechanisms, by predicting the potential inefficacy of a therapeutic phage and thus improving patient prognosis.

Abstract Drug approvals involving novel mechanism-of-action targets currently account for about one-fifth of new FDA-approved drugs each year. Developing therapies for novel targets carries added risks, but they can significantly address areas with unmet medical needs, or current treatment limitations. The Open Targets Platform is a valuable, regularly updated, open resource for identifying and prioritising therapeutic targets, integrating diverse data sources with a user-friendly interface. However, it lacks assessment of target novelty and has minimal timestamping. In response, we implemented comprehensive timestamping across millions of biomedical data points and introduced a metric to summarise the novelty of a target in the context of disease(s) to discover novel drug targets within the Open Targets ecosystem. A retrospective analysis of novel drug target approvals since 2000 suggests that the genetic evidence for clinical progression is increasingly considered earlier in the pipeline, highlighting the benefit of assessing association evidence in the context of time.

We develop Spatial Perturb-Seq, an in vivo CRISPR technology that interrogates multiple genes within single cells of intact tissues. We apply Spatial Perturb-Seq to screen risk genes for neurodegenerative diseases in the mouse brain, uncovering cell autonomous and cell-cell microenvironmental effects within the spatially intact tissue. Spatial Perturb-Seq functionally screens multiple genes in situ and in vivo , identifying candidate genes underlying dysregulated neuronal intercellular communication pathways in Lrp1 signalling and ephrin-Eph receptor interactions.

Modeling and simulating gene regulatory networks (GRNs) is crucial for understanding biological processes, predicting system behavior, guiding the design of synthetic biological systems, and interpreting experimental data. In synthetic biology, GRNs play a pivotal role in enabling the design and control of complex systems for a wide range of applications. However, GRN simulations can be time-consuming and often require specialized expertise. To make this process more accessible, we developed a user-friendly application with a graphical user interface (GUI), allowing users to create simple phenomenological models without requiring prior programming experience. We demonstrate the versatility of our tool through several examples, including the design of novel oscillator families capable of robust oscillation with an even number of nodes. These complement the well-known repressilator family, which only oscillates with odd-numbered nodes. Furthermore, we showcase how GRN modeler allowed us to develop a light-detecting biosensor in Escherichia coli that can track light intensity over several days, leaving a record in the form of ring patterns in bacterial colonies. In summary, our work empowers biologists to model their systems of interest even without programming expertise.

Abstract Cornelia de Lange Syndrome (CdLS) is a prevalent cohesinopathy, frequently arising from mutations in genes encoding components of the cohesin complex, with NIPBL being the most commonly affected. This study aimed to investigate the consequences of a 5' untranslated region (UTR) mutation (c.-467 C > T) in the NIPBL gene on gene expression, cohesin complex integrity, and cellular development. Utilizing CRISPR/Cas9 technology, we generated a heterozygous cell line harboring the NIPBL 5'UTR mutation and employed a suite of molecular biology techniques, including RNA secondary structure prediction, luciferase reporter assays, and RT-pcr, to evaluate the mutation's impact. Our findings indicate that the 5'UTR mutation introduces an additional upstream open reading frame (uORF), resulting in diminished mRNA and protein expression levels of NIPBL . This reduction in NIPBL expression correlated with a downregulation of RAD21, a pivotal component of the cohesin complex, and a decrease in nuclear β-catenin levels, thereby affecting cell proliferation. This study elucidates that the 5'UTR mutation in NIPBL contributes to CdLS by disrupting gene expression and cellular processes, underscoring the significance of 5'UTR elements in the regulation of gene expression and the potential ramifications of sequence variations within this region. Our results advance the understanding of the molecular mechanisms underlying CdLS and may inform the development of targeted therapeutic interventions.

Anopheles funestus s.s. is a formidable human malaria vector across sub-Saharan Africa. To understand how the species is evolving, especially in response to malaria vector control, we sequenced 656 modern specimens (collected 2014-2018) and 45 historic specimens (collected 1927-1967) from 16 African countries. We find high levels of genetic variation with clear and stable continental patterns. Six segregating inversions might be involved in adaptation of local ecotypes. Strong recent signals of selection centred on canonical insecticide resistance genes are shared by multiple populations. A promising gene drive target in An. gambiae is highly conserved in An. funestus . This work represents a significant advance in our understanding of the genetic diversity and population structure of An. funestus and will enable smarter targeted malaria control.

Abstract Prostate cancer (PCa) is the most common malignancy in men worldwide, with an increasing incidence rate, and many patients are diagnosed at an advanced stage with metastasis, where bone metastasis is the most frequent. Enzalutamide (ENZ) is the first-line treatment for castration-resistant prostate cancer (CRPC) and has shown efficacy in prolonging survival; however, some patients develop drug resistance. Additionally, benign prostatic hyperplasia (BPH) is a common prostate condition in aging men, with symptoms similar to PCa, highlighting the need for improved diagnostic and therapeutic approaches. In the present study, we integrated public databases, RNA sequencing (RNA-Seq), and bioinformatics tools, utilizing CRISPR-Cas9 technology to knock out galectin-1 (LGALS1) in PCa cells to comprehensively investigate its impact on ENZ sensitivity, cellular functions, and the underlying mechanisms. Clinical tissue samples were also analyzed to assess the clinical significance of LGALS family members. Our findings indicated that ENZ sensitivity depends on AR expression, and LGALS1 knockout in AR-expressing cells enhances ENZ sensitivity. RNA-Seq revealed that LGALS1 knockout suppresses energy metabolism and disrupts oxidative stress balance. Additionally, LGALS1 knockout in high-expression cells reduced proliferation, altered the cell cycle, and decreased migration and adhesion. Clinically, both AR and LGALS1 were overexpressed in bone-metastatic PCa, suggesting their potential as therapeutic targets and biomarkers.

Abstract Enteroendocrine cells (EECs) are specialized intestinal hormone-secreting cells that play critical roles in metabolic homeostasis, digestion, and gut-brain communication. They detect diverse stimuli including endocrine, immune, neuronal, microbial, and dietary signals, through a complex array of receptors, ion channels, and transporters, to modulate the release of over 20 hormones. These molecular sensors serve as potential drug targets to modulate hormone secretion, but until recently, catalogues of such targets in human colonic EECs have not been produced. To address this gap, we performed bulk and single-cell RNA sequencing on fluorescently labelled EECs isolated from human colonic organoids, identifying and cataloguing potential druggable targets. This catalogue includes receptors, orphan GPCRs, transporters, and hormones not previously reported in human colonic EECs. Comparison with murine EECs highlighted interspecies similarities and differences, key data to facilitate the design and optimise the predictive accuracy of pre-clinical models. We also functionally validated two receptors not previously identified in human EECs: IL-13Rα1, was expressed in both peptide-producing EECs and serotonin producing Enterochromaffin cells (ECs), and its ligand IL-13 stimulated the secretion of glucagon-like peptide-1 (GLP-1) and serotonin measured in real-time, and GPR173, which was selectively expressed in ECs and, when activated by its agonist Phoenixin-20, also promoted serotonin release. These analyses provide a valuable resource for therapeutic interventions aimed at modulating gut hormone secretion, with potential applications in treating gastrointestinal, metabolic, and other related disorders.

Abstract Viruses rely on egress machinery for cell exit, which is crucial for their transmission. While non-enveloped RNA viruses, such as picornaviruses, are typically associated with the lytic release pathway, emerging evidence suggests they can also be packaged within vesicles for non-lytic release. However, the molecular mechanisms regulating this remain unclear. Here, we performed a genome-wide CRISPR-Cas9 screen and identified the microRNA hsa-miR-3156-1 as a critical host factor for picornavirus replication. Both the primary and mature forms of miR-3156-1 were upregulated following infection, with miR-3156-3p serving as a positive regulator of viral replication by directly targeting the 3′-untranslated regions of K+ channel-associated genes, KCNV1, KCNJ2, KCNK3, and KCNK5, causing plasma membrane depolarization and Ca2+ influx, which facilitate non-lytic release. Administration of a miR-3156-3p antagomir alleviated virus-associated acute flaccid paralysis in a mouse model. Our findings reveal how the miR-3156-3p/K+ channel regulatory axis regulates picornavirus release, highlighting potential therapeutic targets.

Genome editing enables sequence-function profiling of endogenous cis-regulatory elements, driving understanding of their mechanisms and the development of gene therapies. However, these approaches cannot be combined with direct scalable readouts of chromatin structure and accessibility across long single-molecule chromatin fibers. Here we leverage a double-stranded DNA cytosine deaminase to profile chromatin accessibility at high depth and resolution at endogenous loci of interest through targeted PCR and long-read sequencing, a method we term targeted deaminase-accessible chromatin sequencing (TDAC-seq). Powered by high sequence coverage at targeted loci of interest, TDAC-seq can be uniquely integrated with CRISPR perturbations to enable the functional dissection of cis-regulatory elements, where genetic perturbations and their effects on chromatin accessibility are superimposed on the same single chromatin fiber and resolved at single-nucleotide resolution. We employed TDAC-seq to parse CRISPR edits that activate fetal hemoglobin in human CD34+ hematopoietic stem and progenitor cells during erythroid differentiation as well as in pooled CRISPR and base editing screens tiling an enhancer controlling the globin locus. Together, TDAC-seq enables high-resolution sequence-function mapping of single-molecule chromatin fibers by genome editing.

Generative genomics models can design increasingly complex biological systems. However, effectively controlling these models to generate novel sequences with desired functions remains a major challenge. Here, we show that Evo, a 7-billion parameter genomic language model, can perform function-guided design that generalizes beyond natural sequences. By learning semantic relationships across multiple genes, Evo enables a genomic “autocomplete” in which a DNA prompt encoding a desired function instructs the model to generate novel DNA sequences that can be mined for similar functions. We term this process “semantic mining,” which, unlike traditional genome mining, can access a sequence landscape unconstrained by discovered evolutionary innovation. We validate this approach by experimentally testing the activity of generated anti-CRISPR proteins and toxin-antitoxin systems, including de novo genes with no significant homology to any natural protein. Strikingly, in-context protein design with Evo achieves potent activity and high experimental success rates even in the absence of structural hypotheses, known evolutionary conservation, or task-specific fine-tuning. We then use Evo to autocomplete millions of prompts to produce SynGenome, a first-of-its-kind database containing over 120 billion base pairs of AI-generated genomic sequences that enables semantic mining across many possible functions. The semantic mining paradigm enables functional exploration that ventures beyond the observed evolutionary universe.

Although the species is extensively studied, limited data are available on antiphage defense systems (APDSs) in Streptococcus mutans . The present study aimed to explore the diversity and the occurrence of APDSs and to search for prophages in the genomes of clinical isolates of S. mutans using bioinformatics tools. Forty-four clinical isolates of S. mutans were obtained from saliva samples of people with Parkinson’s disease. Genomic DNA was extracted, sequenced using Illumina MiSeq technology, and analyzed for the presence of defense systems using DefenseFinder. CRISPR- Cas systems were characterized using CRISPRCasFinder, and prophages were detected by the PhiSpy pipeline from RAST. AcrFinder and AcrHub were used to identify anti-CRISPR proteins. Each strain harbored between 6 and 12 APDS, with restriction-modification systems being the most prevalent, followed by the MazEF toxin-antitoxin system and CRISPR-Cas systems. Type II-C CRISPR-Cas systems were not identified here in S. mutans . Novel variations in type II-A signature protein Cas9 were identified, allowing their classification into four distinct groups. Variability in direct repeat sequences within the same CRISPR array was also observed, and 80% of the spacers were classified as targeting "dark matter". A unique prophage, phi_37bPJ2, was detected, showing high similarity with previously described phages. The AcrIIA5 protein encoded by phi_37bPJ2 was conserved and suggested to remain functionally active. This study reveals the diversity of APDSs in S. mutans and the limited presence of prophages. The findings provide a foundation for future research on the evolutionary dynamics of these systems and their role in S. mutans adaptation to phage pressure.

ABSTRACT In cattle, communication between endometrium and conceptus during the peri-implantation period is crucial for successful pregnancy. Understanding these interactions is vital as most early pregnancy loss occurs during this time. A major challenge in understanding uterine function and early pregnancy is lack of appropriate in-vitro models. Two-dimensional models are available, but do not recapitulate the endometrium’s complex multicellular structure. Here, we describe a hormonally responsive organoid model of the bovine endometrium, developed as a tool for studying endometrial function and early pregnancy. Bovine glandular epithelial cells were isolated from reproductive tracts and cultured in an extracellular matrix hydrogel (Cultrex 2) at 38.5°C, 5% CO (n=3). RNA was extracted and qPCR confirmed the presence of gland markers: leukemia inhibitory factor, mucin-1, insulin-like growth factor binding protein-1, kruppel-like factor-5 and forkhead box protein-A2 . Organoids were imaged at specific time-points to monitor growth and passaged 3 times in 1:2 or 1:3 ratios after growing for a minimum of 10 days per passage. Morphologically, organoids were spherical and fast-growing at passages 0 and 1, but this declines following passage 2. Bovine endometrial organoids (n=3, passage 0) were treated with 1000 ng/ml recombinant ovine Interferon Tau (IFNT) or 10 μg/ml progesterone (P4) for 24 hours and analysed by RNASeq to assess hormone responsiveness. Differential expression analysis by DeSeq2 negative binomial distribution model followed by Wald test and Benjamini-Hochberg correction identified 373 transcripts significantly upregulated (padj 0.05) in response to P4 treatment, with downstream analysis showing significant overrepresentation (FDR<0.05) of genes associated with positive regulation of protein localisation to plasma membrane and cell periphery. Of the 240 genes significantly downregulated by P4 these were significantly overrepresented (FDR<0.05) in biological processes of cilium and cytoskeleton organisation. IFNT treatment resulted in significant upregulation of 414 genes and downregulation of 119 genes. The largest cluster associated with differentially expressed genes in response to IFNT is defence to virus and interferon signalling. There were 30 genes altered by both P4 treatment and IFNT treatment. Organoids were also shown to express conserved microRNAs, and it was possible to culture them in a microfluidics device - making them a useful model for a multitude of potential investigations. This model provides a tool to investigate bovine endometrial function and peri-implantation communication, subsequently allowing species comparison to understand diversity in reproductive strategies.

Anti-sense oligonucleotides (ASOs) are modified synthetic single-stranded molecules with enhanced stability, activity, and bioavailability. They associate with RNA through sequence complementarity and can reduce or alter mRNA expression upon binding of splice site positions. To target RNA in the nucleus or cytoplasm, ASOs must cross membranes, a poorly understood process. We have performed an unbiased CRISPR/Cas9 knockout screen with a genetic splice reporter to identify genes that can increase or decrease ASOs activity, resulting in the most comprehensive catalog of ASOs-activity modifier genes. Distinct targets were uncovered, including AP1M1 and TBC1D23, linking ASOs activity to transport of cargo between the Golgi and endosomes. AP1M1 absence strongly increased ASO activity by delaying endosome-to-lysosome transport in vitro and in vivo . Prolonged ASOs residence time in the endosomal system may increase the likelihood of ASOs escape from this organelle before they reach lysosomes. This insight into AP1M1 role in ASOs trafficking suggests a way for enhancing the therapeutic efficacy of ASOs by manipulating the endolysosomal pathways.

The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune responses in the type III CRISPR-Cas systems. Whereas most previously characterized CARF proteins contain nucleic acids or protein degradation effectors, a subset comprises C ARF-fused a denosine d eaminase (ADA) (Cad1) and has a yet to be determined function. Here we present biochemical and structural analyses of a ring nuclease Cad1, revealing its unexpected role in deaminating adenosine-5′-triphosphate to inosine-5′-triphosphate in a cOA-dependent manner. Despite an overall structural similarity to canonical ADA enzymes, the ADA domain of Cad1 possesses unique structural features underlying its specificity for ATP. Supported by mutational analysis, we demonstrate an allosteric link between the cOA-binding CARF and the ADA domain, suggesting that Cad1 is a cOA-stimulated effector that influences cellular metabolic processes. Highlights TaqCad1 converts ATP to ITP in a magnesium- and cOA-dependent manner Cryo-EM structures reveal TaqCad1 forms a homohexamer Cryo-EM structures reveal how cA 4 is degraded and modulates the ADA active site

In vitro human organoid models have become transformative tools for studying organogenesis, enabling the generation of spinal cord organoids (SCOs) that mimic aspects of spinal cord biology. However, current models do not produce spinal motor neurons (spMNs) with a wide range of axial identities along spinal cord segments within a single structure, limiting their utility in understanding human neural axial specification and the selective vulnerability of spMN subpopulations in motor neuron diseases. Here, we present a novel approach to enhance spMN axial heterogeneity in an advanced SCO model derived from neural stem cells (NSCs) and retinoic acid (RA)-primed neuromesodermal progenitors (NMPs). RA priming guided NMP differentiation into caudal neural progenitors, generating SCOs enriched in spMNs with posterior axial identities. To further diversify spMN populations, we optimized differentiation by synchronously patterning NSCs with RA-primed NMPs. Incorporating an endothelial-like network and skeletal muscle cells enhanced the organoids’ physiological complexity and neural maturation and organoid cell viability. This comprehensive approach, termed CASCO, provides a robust platform to study human spMN specification and model neurodegenerative diseases.

Downstream of oncogenic RAS, RALA is critical for cancer tumorigenesis, possibly regulated by phosphorylation of its Serine194 residue. We made CRISPR-Cas9 RALA knockout (RALA KO) in three RAS-dependent and two RAS-independent cancer cells. Detection of RALA S194 phosphorylation using the commercial anti-phospho-RALA antibody lacks specificity in all three RAS-dependent cancers. siRNA knockdown of RALA and AURKA inhibition by MLN8237 (V MLN ) also did not affect pS194RALA detection in these cancers. RALA KO MiaPaCa2 (RAS-dependent) and MCF7 (RAS-independent) cells, stably reconstituted with WT-RALA and S194A-RALA mutants, showed no effect on RALA activation. Tumour growth was, however, restored partly by WT-RALA, but not S194A-RALA mutant. Thus, RALA S194 phosphorylation is needed for tumor formation, not affecting its activation but possibly through its localization.