ABSTRACT Chromatin is dynamic at all length scales, influencing chromatin-based processes, such as gene expression. Even large-scale reorganization of whole chromosome territories has been reported upon specific signals, but lack of suitable methods has prevented analysis of the underlying dynamic processes. Here we have used CRISPR-Sirius for time-lapse imaging of chromatin loci dynamics during serum starvation. We show that the chromosome 1 loci move towards the nuclear envelope during the first hour of serum starvation in a chromosome-specific manner. Machine learning-assisted exploration of acquired multiparametric data combined with the Shapley values-based explanation approach allowed us to uncover the critical features that characterize chromatin dynamics during serum starvation. This analysis reveals that although serum starvation affects overall nuclear morphology and chromatin dynamics, chromosome 1 loci display a specific response that is characterized by maintenance of dynamics in constrained environment, and long “jumps” at the nuclear periphery. Interestingly, the two homologous chromosomes display differential behaviors, with the more peripheral homolog being more responsive to the signal than the internal one. Overall, the presented machine learning-assisted dataset exploration helps us navigate the multidimensional data to understand the underlying dynamic processes and can be applied to a wide variety of research questions in imaging and cell biology in general.

CRISPR/Cas9 has revolutionized genome editing with broad therapeutic applications, yet its repair patterns in vivo remain poorly understood. Here, we systematically profiled CRISPR/Cas9 editing outcomes at 95 loci using our established CRISPR/Cas9/AAV9-sgRNA system in skeletal muscle stem cells (MuSCs). Through comprehensive characterization of the repair outcomes, our findings demonstrate that the general rules governing CRISPR/Cas9-mediated editing in vivo largely align with those observed in vitro but with reduced editing precision. Additional to the anticipated small editing indels such as MMEJ mediated deletions and NHEJ mediated templated insertions, we uncovered a prevalent occurrence of large on-target modifications, including large deletions (LDs) characterized by microhomology (MH) and large insertions (LIs). Notably, the LIs comprise not only exogenous AAV vector integrations but also endogenous genomic DNA fragments (Endo-LIs). Endo-LIs preferentially originate from active genomic regions, with their integration shaped by three-dimensional chromatin architecture. By disrupting key components of the NHEJ and MMEJ repair pathways in vivo , we identified their distinct roles in regulating the large on-target modifications. Together, our work for the first time systematically profiles the CRISPR/Cas9 repair outcomes in vivo and offers valuable guidance for improving the safety of CRISPR/Cas9-based gene therapies.

Deciphering spatiotemporal cell lineage dynamics remains a fundamental yet unresolved challenge. Here we introduce eTRACER, a novel CRISPR-Cas9 lineage tracer that targets neutral 3’UTR of high-expression endogenous genes, enabling efficient recovery of static and evolving barcodes from single-cell and spatial transcriptomics. By optimizing gradient editing efficacy and avoiding large disruptive deletions, eTRACER reconstructs high-fidelity and high-resolution single-cell phylogenies. Applied to EGFR-mutant lung adenocarcinoma (LUAD) under CD8 + T cell cytotoxicity, eTRACER reveals directional state transitions from Hypoxic and Proliferative states to Epithelial-Mesenchymal Transition state during immune evasion. Spatially-resolved lineage mapping unveils layered stratification of distinct tumor states and location-primed cell migration and state transitions. Lineage-coupled single-cell multiomic analysis uncovers cooperative mechanism between tumor cell-intrinsic AP-1 transcriptional program and spatially restricted macrophage-tumor cell interaction leading to immune evasion. Collectively, we develop a powerful spatiotemporal lineage tracer and uncover microenvironment-primed cellular evolution underlying immune evasion of EGFR-mutant LUAD, with important implication for efficient immunotherapy.

Reverse genetics, facilitated by CRISPR technologies and comprehensive sequence-indexed insertion mutant collections, has advanced the identification of plants genes essential for arbuscular mycorrhizal (AM) symbiosis. However, a mutant phenotype alone is generally insufficient to reveal the specific role of the protein in AM symbiosis and in many cases, identifying interacting partner proteins is useful. To enable identification of protein:protein interactions during AM symbiosis, we established a Medicago truncatula -Diversispora epigaea yeast-two-hybrid (Y2H) library which, through Y2H-seq screening, can provide a rank-ordered list of candidate interactors of a protein of interest. We also developed a vector system to facilitate bimolecular fluorescence complementation assays (BIFC) in mycorrhizal roots so that protein interactions can be assessed in their native cell types and sub-cellular locations. We demonstrate the utility of a Y2H-seq screen coupled with BIFC in mycorrhizal roots, with a search for proteins that interact with CYCLIN DEPENDENT LIKE KINASE 2 (CKL2), a kinase essential for AM symbiosis. The Y2H-seq screen identified three 14-3-3 proteins as the highest ranked CKL2 interacting proteins. BIFC assays in mycorrhizal roots provided evidence for a CKL2:14-3-3 interaction at the periarbuscular membrane (PAM) in colonized root cells. Down-regulation of 14-3-3 by RNA interference provides initial evidence for a function in AM symbiosis. Thus, CKL2 may utilize 14-3-3 proteins to direct signaling from the PAM. The Y2H and BIFC resources will accelerate understanding of protein functions during AM symbiosis.

Strigolactones are ecologically, developmentally, and physiologically important hormones, but much remains unknown about their evolution and role in non-model species. Sorghum is an important C 4 cereal for ∼1 billion people globally and exhibits natural variation in root-exuded strigolactones. Differences in sorghum strigolactone stereochemistry are associated with resistance to a parasitic plant, but with evidence for potential trade-offs. In the present study, we studied sorghum mutants of loci in the strigolactone biosynthetic pathway, C AROTENOID CLEAVAGE DIOXYGENASE 8 ( CCD8 ) and LOW GERMINATION STIMULANT 1 ( LGS1 ). We found that CCD8 CRISPR-Cas9 deletions changed the accumulation of low abundance metabolites, reduced net carbon assimilation rate, altered root architecture and anatomy, and reduced the establishment and benefit of mycorrhizal symbionts. For LGS1 CRISPR-Cas9 deletions, we found net carbon assimilation rate to be reduced, the colonization of mycorrhizal symbionts to be delayed, and evidence for regulatory pathways involved in stress response and growth to be impacted. We further tested the impacts of restoring functionality of LGS1 into a normally non-functional background (RTx430). Notably, we did not see consistent impacts of LGS1 loss-of-function across LGS1 deletion and insertion mutants, though root exudates from insertion mutants increased stimulation of Striga germination, suggesting that background specific modifiers may buffer the strigolactone impacts of loss-of-function at LGS1 . Our study begins to give context to the trade-offs associated with a host resistance strategy to a parasitic plant and more broadly contributes to understanding the role strigolactones play in sorghum physiological processes, growth, and development.

ABSTRACT Background The histone chaperone complex, consisting of the death domain–associated protein (DAXX) and the alpha-thalassemia/mental retardation X-linked protein (ATRX), plays a pivotal role in maintaining chromatin through the deposition of the histone variant H3.3. Mutations leading to loss of ATRX or DAXX function are linked to the non-telomerase, alternative lengthening of telomeres (ALT) phenotype in certain cancers. Engineered ATRX mutations have previously been found to induce features of ALT in prostate cancer cell lines, notably in LAPC-4, but not in CWR22Rv1. This study determined the impact of DAXX mutations on ALT-associated characteristics in CWR22Rv1 and LAPC-4. Methodology Mutations were induced in CWR22Rv1 and LAPC-4 cells by targeting exon 2 of DAXX using the CRISPR-Cas9 genome editing strategy. The resulting mutant clones were then evaluated for ALT-associated characteristics, including the presence of ALT-associated PML bodies (APBs), C-circles, telomere length heterogeneity, and a lack of telomerase activity. Results Four CWR22Rv1 DAXX mutant clones ( DAXX Mut 1 - 4 ) and five LAPC-4 clones ( DAXX Mut 1-5 ) were evaluated. In CWR22Rv1, DAXX Mut 1, DAXX Mut 2, and DAXX Mut 4 were true knockout clones with frameshift mutations in both copies, while CWR22Rv1 DAXX Mut 3 had a frameshift mutation in one copy and an in-frame mutation in the other. Protein expression was undetectable in all the CWR22Rv1 clones, including CWR22Rv1 DAXX Mut 3 . In LAPC-4, DAXX Mut 1 was a true knockout, while DAXX Mut 2, DAXX Mut 3, DAXX Mut 4 , and DAXX Mut 5 clones had at least one in-frame mutation. Among these LAPC-4 clones, only DAXX Mut 1 had undetectable protein by western blotting. ALT-associated characteristics such as APBs, C-circles, and telomere length heterogeneity were observed only in CWR22Rv1 DAXX Mut 4 . All the clones maintained telomerase activity, regardless of whether ALT-associated hallmarks were observed. Implications The CWR22Rv1 and LAPC-4 DAXX mutant clone models provide useful tools for future studies on telomere maintenance mechanisms and DAXX-related biology, particularly in prostate cancer.

Abstract Here we report unprecedented efficacy in the functional repair of an exemplar locus, ornithine transcarbamylase (OTC), in mutant primary mouse and human hepatocytes in vivo using a dual AAV vector system configured to deliver CRISPR-Cas9 editing reagents and a promoterless donor for targeted integration by non-homologous end joining. The approach was mutation agnostic and targeted editing events to intronic sequences to prevent inadvertent inactivation of hypomorphic alleles. Notably, in a murine model, we corrected the metabolic defect and simultaneously achieved liver-wide restoration of physiological metabolic zonation of OTC expression by capture of the native promoter. The effectiveness of this approach was confirmed using a universally configured therapeutic cassette in patient-derived primary human hepatocytes in vivo. These data provide a powerful template to guide further optimization of this approach and, given the high editing efficacy required for phenotypic effect in OTC deficiency, have broader relevance to other liver disease phenotypes.

Abstract We have developed a CRISPR/Cas based assay able to distinguish between two ranges of closely related RNA targets using two detection channels. This required a pipeline to design RNA guide sets with the right degree of specificity. We tested our approach using SARS-CoV-2 and zoonotic near-neighbor sarbecoviruses. Using pre-existing guide design rules, we utilized a machine learning based model to design and optimize guide sets for specific detection of SARS-CoV-2 and separately to its nearest neighbors. The in vitro testing of the guide sequences has shown that Cas13 assays can tolerate more mismatches than assumed based on previous guide design rules. Mismatches located closer to the 3’ end of the guide and mismatches evenly distributed throughout the guide resulted in a smaller impact on the guide’s ability to activate the Cas enzyme. Modified SHERLOCK assay for detection and discrimination of SARS-CoV-2 and its zoonotic coronaviruses was developed using optimized sets of guides. The final assay was able to classify the targets into three classes 1) SARS-Co-V2, 2) closest known SARS-Co-V2 near-neighbor BANAL-236 and 3) the remaining zoonotic near-neighbors. This approach provides value through early detection of natural and engineered variants.

Despite the growing catalog of long noncoding RNAs (lncRNAs), the functional roles of their vast majority in cancer remain poorly defined. To systematically explore lncRNA dependencies in triple-negative breast cancer (TNBC), we compiled a comprehensive annotation by merging GENCODE, BIGTranscriptome, and MiTranscriptome databases and performed a CRISPR-Cas9 deletion screen targeting 1,029 TNBC-enriched lncRNAs. The screen revealed several essential lncRNAs and those modulating doxorubicin sensitivity, with TPL1 emerging among top hits. TPL1 silencing significantly impaired TNBC cell proliferation in both 2D and 3D cultures and reduced invasive capacity in an organ-on-chip model. Transcriptomic and proteomic profiling following TPL1 knockdown revealed downregulation of genes involved in ECM–receptor interaction, focal adhesion, cell migration, and PI3K-Akt signaling. Mechanistically, TPL1 directly interacted with key proteins including EIF4B, MDM2, TARBP2, TLE5, and GTPase RAN, suggesting TPL1 could regulate RNA processing, transcriptional repression, and translation, as well as modulate GTPase signaling pathways. Additionally, TPL1 functioned as a competing endogenous RNA (ceRNA), sequestering miR-10396b-5p, miR-486-3p, and miR-450a-2-3p, among others, thereby modulating expression of pro-tumorigenic targets. Clinically, TPL1 was significantly overexpressed in TNBC tissues, particularly in the BLIS subtype. Collectively, our findings highlight TPL1 as a key regulator of TNBC molecular networks and a promising therapeutic target.

Precise regulation of transcription factor (TF) expression is critical for maintaining cell identity, but studies on how graded expression levels affect cellular phenotypes are limited. To address this gap, we employed human embryonic stem cells (hESCs) as a dynamic model to study gene dosage effects and systematically titrated key TFs NANOG and OCT4 expression using CRISPR interference (CRISPRi). We then profiled transcriptomic changes in hESCs under self-renewal and differentiation conditions using single-cell RNA-seq (scRNA-seq). Quantitative modeling of these Perturb-seq datasets uncovers distinct response patterns for different types of genes, including a striking non-monotonic response of lineage-specific genes during differentiation, indicating that mild perturbations of hESC TFs promote differentiation while strong perturbations compromise it. These discoveries suggest that fine-tuning the dosage of stem cell TFs can enhance differentiation efficiency and underscore the importance of characterizing TF function across a gradient of expression levels.

Cyclin-Dependent Kinase 4 (CDK4) is a key regulator of cell cycle progression, driving the G0/G1-to-S phase transition through phosphorylation of Retinoblastoma 1 (RB1). Clinically, CDK4/6 inhibitors are under investigation in Triple Negative Breast Cancer (TNBC), a subtype characterized by invasiveness, aggressiveness and poor prognosis. While CDK4 is primarily targeted for its role in proliferation, emerging evidence suggests it may also regulate other cellular processes. In particular, the mechanisms by which CDK4 could influence cancer cell migration, remain largely unexplored, particularly in highly heterogenous cell line like MDA-MB-231. This study investigates whether CDK4 contributes to the regulation of TNBC cells migration and identifies the pathways involved in MDA-MB-231 cells, independently of its role in proliferation. We demonstrate that loss or inhibition of CDK4, using respectively CRISPR/Cas9 mediated CDK4 knockout and pharmacological CDK4/6 inhibitor, leads to enhanced migration capacities and reorganization of actin subcellular networks. Mechanistically, the absence of CDK4 results in decreased phosphorylation of Myo9b at serine 1935 (S1935), which enhances RhoA signaling, a key driver of cytoskeletal dynamics, leading to polarity defects and increased cell migration. These findings reveal a non-canonical function of CDK4 in limiting TNBC cell migration through the CDK4/CyclinD-Myo9b-RhoA signaling axis. This work highlights the broader cellular roles of CDK4 beyond its established function in proliferation and suggest that inhibition of Myo9b-RhoA pathway could reduce metastatic behaviour in TNBC treated with CDK4/6i, thereby informing future co-therapeutic strategies against aggressive cancer subtypes.

Summary The CRISPR-Cas9 system has been widely adopted as a genome editing tool due to its high efficiency and versatility, contributing to the development of various therapeutic strategies. However, its clinical application remains limited by safety concerns, including off-target effects and large-scale chromosomal rearrangements such as translocations and inversions. Recently, the CRISPR-Cas3 system, a Class 1 CRISPR effector complex with unidirectional DNA degradation activity, has gained attention as a potential alternative, offering reduced off-target activity. In this study, we applied the CRISPR-Cas3 system to human T cells and successfully disrupted two clinically relevant genes, T cell receptor alpha constant (TRAC) and beta-2 microglobulin (B2M). These gene deletions were associated with a reduction in both graft-versus-host disease (GVHD) risk and host immune rejection. Importantly, no off-target mutations were detected in CRISPR-Cas3-edited cells, in contrast to the off-target effects observed with CRISPR-Cas9. Furthermore, CAR-T cells generated by deleting TRAC or B2M using CRISPR-Cas3 maintained their antigen-specific cytotoxicity against tumor cells, while exhibiting reduced alloreactivity. These results suggest that CRISPR-Cas3 provides a safer and promising platform for genome editing in T cell engineering, with potential applications in the development of next-generation allogeneic T cell therapies.

Nutritional immunity is an antimicrobial strategy that evolved to starve pathogens of essential nutrients, with death as the desired outcome. Here, we report that transient iron starvation of the obligate intracellular pathogen Chlamydia trachomatis , growing in endocervical epithelial cells, enhances pathogen recognition by the host cell through the dysregulation of a peptidoglycan (PG) remodeling enzyme, resulting in the activation of the nucleotide-binding oligomerization domain 2 (NOD2) pathway that recognizes PG fragments, increased production of tumor necrosis factor alpha (TNF) via increased activation of NF-κB, which correlated with death of infected cells. Activation of the NOD2/ NF-κB signaling axis is linked to the dysregulated overexpression of the PG remodeling enzyme AmiA and the subsequent cleavage and mislocalization of D-Ala-D-Ala analog. Inhibiting amiA transcriptional upregulation by CRISPR interference reduced pathogen recognition. We propose that nutritional immunity in general mediate abnormal expression of bacterial genes linked to pathogen-associated molecular patterns. Importance Limiting pathogen access to essential nutrients is the central tenet of nutritional immunity, with the outcome being severe starvation and eventual death of the pathogen. However, pathogen starvation induces several physiological changes prior to its death. They include errors in several biological processes, including metabolism and gene expression, which could lead to pathogen death. Here, we demonstrate that iron starvation of the clinically relevant human pathogen Chlamydia trachomatis significantly dysregulates the expression of a peptidoglycan remodeling amidase, AmiA to enhance chlamydial recognition by the host cell and the subsequent increased production of tumor necrosis factor and death of infected cells to the detriment of Chlamydia .

Abstract RNA-level detection is a critical approach for determining whether genetic variants affect splicing and for identifying potential pathogenic variants. However, tissues where disease-causing genes are expressed are often difficult to obtain in routine testing, while readily accessible tissues like blood do not express all disease-causing genes. CRISPR activation (CRISPRa) is a powerful technique for activating endogenous gene expression, and its application in peripheral blood mononuclear cells (PBMCs) offers an effective strategy for RNA analysis. In this study, we used CRISPRa to activate the expression of three disease-associated genes— FBN1 , F8 , and DMD —in PBMCs, achieving upregulation of target gene expression within 48 hours. In patient-derived cells, activation of FBN1 expression revealed that a deletion of exons 48–53 leads to a 708-bp in-frame deletion variant at the mRNA level. Notably, this CRISPRa-based method enabled the validation of splicing site variants within 3 days, significantly reducing turnaround time for clinical testing. Furthermore, we successfully activated 83 common disease-causing genes and established a single-guide RNA (sgRNA) library platform for activatable genes. This resource facilitates broader validation and screening of splicing site variants. Overall, this is the first study to demonstrate the use of CRISPRa for RNA-level variant detection in patient PBMCs. Our approach provides a novel approach for validating splicing site variants, including variants of unknown significance, as pathogenic in real clinical settings.

Severe loss of function variants in the splicing regulatory protein RBM10 are known to cause TARP syndrome, a rare X-linked recessive congenital syndrome. In recent years, individuals with milder phenotypes have been published, suggesting a broader phenotypic spectrum. We report 37 new individuals with RBM10 variants and compare to 34 published cases. We find that the phenotype can be described as an “RBM10-phenotypic spectrum” which can be further subdivided into two phenotypic groups, TARP syndrome (TARPS) and RBM10 Associated Intellectual Disability (RAID). Based on phenotype characterizations and functional studies, we describe a clear genotype-phenotype correlation. Splicing analysis of blood samples and CRISPR-edited cells representing different degrees of functional loss of RBM10 demonstrated a pattern of more exon inclusion in response to increased loss of RBM10 function. More inclusion was correlated with increasing phenotype severity. Functional studies of missense variants from the different phenotypic groups confirm this genotype-phenotype correlation and show that different molecular mechanisms can explain the underlying pathological alterations in RBM10 protein function. Interestingly, we show that some missense variants in the RNA binding, RRM2 domain of RBM10 alter RBM10 activity from splicing inhibition to stimulation, likely due to altered RNA binding characteristics. Graphical Abstract

Cocaine use disorder is highly comorbid in people with HIV and can accelerate infection, alter neuropathology, and exacerbate cognitive decline despite antiretroviral therapy (ART). Many of these effects are due to infection and dysregulation of CNS myeloid cells, especially microglia, which comprise a significant reservoir in this compartment. However, the precise mechanism(s) by which cocaine (Coc) enhances HIV infection in microglia are unclear, partly due to the lack of translationally relevant human microglial models suitable for mechanistic evaluation of Coc-mediated changes in viral dynamics. Canonically, Coc acts by blocking dopamine transporter activity, however, Coc has additional mechanisms beyond dopaminergic tone, involving the endoplasmic reticulum (ER) protein sigma-1, which has diverse cellular functions, including modulation of stress pathways such as the unfolded protein response (UPR). Viruses, including HIV, can exploit the UPR to amplify stress-induced protein production in host cells, enhancing viral replication. Therefore, we hypothesized that Coc-mediated activation of sigma-1 increases HIV infection of microglia via activation of the UPR. Using human-induced pluripotent stem cell microglia (iPSC-Mg), we evaluated changes in the percentage of infected iMg as well as p24Gag secretion using high-content imaging and AlphaLISA. Coc increased both p24 secretion and the number of infected iMg. The enhanced p24 secretion persisted despite ART, without the corresponding increase in percent p24, suggesting Coc augments the post-entry steps of viral replication. Inhibition of dopamine receptors did not diminish the impact of Coc, but pharmacological inhibition and CRISPR KO of sigma-1 blocked the effect. Independently, sigma-1 agonists increased p24 secretion, suggesting that Coc acts through sigma-1 rather than dopaminergic pathways. Single-cell RNA sequencing revealed distinct transcriptomic alterations in HIV+Coc-treated iPSC-Mg. Further genetic and proteomic validation confirmed activation of the IRE1-XBP1 branch of the UPR in the HIV+Coc condition, with increased XBP1 signaling and downstream cytokine (IL-4 and IL-7) secretion. The HIV+Coc condition also showed reduced expression of antiviral response genes and enhanced HIV transcriptional regulation genes. Immunofluorescence staining showed increased sigma-1 in p24-cells and reduced sigma-1 in p24+ cells in HIV+Coc cultures and revealed that HIV+Coc promotes sigma-1 movement to the ER. These findings suggest that Coc exploits sigma-1 signaling to modulate the UPR, enhancing viral replication and immune evasion. Sigma-1 emerges as a critical link between HIV-induced cellular stress and cocaine exposure, highlighting a shared molecular pathway that can be leveraged for the treatment of comorbid HIV neuropathogenesis, substance use disorder, and related neuropsychiatric disorders.

Cryptochromes (CRYs) are photolyase-like blue-light / ultraviolet-A (UV-A) receptors that regulate diverse aspects of plant growth. Maize ( Zea mays ), a major crop often grown under high UV-B radiation, possesses four copies of CRY. However, it remains unclear whether the multiple copies of CRY in maize have evolved to improve UV tolerance or to acquire new functions. In this study, CRISPR-Cas9-engineered Zmcry mutants were used to investigate the functions of four cryptochromes (ZmCRYs) in maize. The findings revealed that ZmCRYs play a redundant role in mediating blue light signaling and in inhibiting the elongation of the mesocotyl. The results also demonstrated that ZmCRYs mediated blue light-enhanced UV-B stress tolerance in Zea mays by upregulating the expression of genes involved in UV-B stress tolerance-related metabolites such as phenylpropanoid, flavonoid, and fatty acid biosynthesis. Furthermore, blue light was found to influence both the accumulation and composition of epidermal waxes, suggesting that blue light enhances epidermal wax accumulation for UV-B stress tolerance. Additionally, it was discovered that ZmCRY1 directly interacted with GLOSSY2 (GL2) in a blue light dependent manner to mediate blue light promoted C32 aldehyde accumulation, shedding new light on the enigma of aldehyde-forming. These results highlight the critical roles of ZmCRY1s in mediating blue light regulated epidermal wax biosynthesis and UV-B tolerance in Zea mays .

Genome wide association study (GWAS) reports substantially outpace subsequent functional characterization. Pinpointing the causal effector gene(s) at GWAS loci remains challenging given the non-coding genomic residency of >98% of these signals. We previously implicated effector genes at GWAS loci for the complex and polygenic disorder of human insomnia using a high-resolution cell-specific, chromatin capture-based variant-to-gene mapping protocol, paired with sleep phenotyping in Drosophila . In this study, we leveraged a diurnal vertebrate model with higher genomic conservation, namely zebrafish, to screen our six highest confidence candidate genes and identify those whose loss-of-function impaired sleep characteristics related to human insomnia-like behaviors. Of these genes, we observed that CRISPR-mediated deletion of the zebrafish ortholog of MEIS1 produced nighttime specific sleep fragmentation and increased latency to sleep, pointing to a conserved role for MEIS1 in sleep maintenance. Comparing our human cell-based chromatin accessibility and contact maps with publicly available zebrafish spatial genomic data revealed highly conserved genomic architecture harboring the insomnia GWAS variant of interest. Notably, this genomic conservation was selective for the zebrafish ortholog which contributed to the sleep phenotype, meis1b, while the duplicated ohnolog meis1a proved dispensable. Motivated by this, we characterized the spatio-temporal expression of meis1b in zebrafish, showing it is comparable to human with respect to cerebellar granule progenitors. Ultimately, we found that loss of meis1b impairs cerebellar development. Together, our work provides a powerful model for screening human disorder risk genes for sleep fragmentation using a tractable vertebrate and supports a conserved cerebellar role for MEIS1 in sleep disturbance.

G protein-coupled receptors (GPCRs) that couple to the Gαq signaling pathway control diverse physiological processes, yet the full complement of cellular regulators for this pathway remains unknown. Here, we report the first genome-wide CRISPR knockout screen targeting a Gαq-coupled GPCR signaling cascade. Using a Drosophila model of adipokinetic hormone receptor (AkhR) signaling, we identified CG34449 (Zdhhc8) , encoding a palmitoyl acyltransferase and its adapter protein CG5447, as a top hit required for robust Gαq-mediated GPCR signaling. We show that Zdhhc8 enhances GPCR signaling through palmitoylation of Gαq, which promotes its membrane localization and function. Loss of Zdhhc8 markedly reduces palmitoylation of Gaq resulting in attenuation of AkhR/Gαq signaling and a reduction in receptor stability. Mechanistically, Zdhhc8 is necessary for palmitoylation of Gαq. These findings uncover Zdhhc8-dependent Gαq palmitoylation as a pivotal regulatory mechanism in GPCR signal transduction and highlight palmitoyl transferase as potential modulators of GPCR pathways.

Abstract 2.1 Background Adipogenesis is a highly organised series of events that facilitates the healthy expansion of adipose tissue, beginning during embryogenesis and continuing throughout life. White adipogenesis protects against lipotoxicity, influencing insulin resistance and obesity-related comorbidities. Brown adipogenesis enhances energy expenditure, thereby counteracting weight gain, lipotoxicity and insulin resistance. Recently, there has been a significant increase in interest regarding adipocyte differentiation, mainly focusing on the interplay between microRNAs (miRNAs) and the transcriptional cascade that governs adipogenesis and metabolic dysfunction. This study aimed to identify miRNAs regulating white and brown adipocyte differentiation and define miRNA action in a stem cell model of adipogenesis. 2.2 Methods Small RNAseq analysis of primary mouse brown and white adipocytes (WAs) identified miR-10b to be upregulated in mature brown adipocytes (BAs). We generated two model systems: 1) immortalized brown pre-adipocytes treated with miRNA inhibitors and 2) CRISPR/Cas9 KO of miR-10b in E14 mouse embryonic stem cells (mESCs). Both cell models were differentiated into mature adipocytes. To unravel the pathways that are affected by miR-10b depletion, a transcriptomic analysis was performed at key time points. 2.3 Results Both cell models showed that miR-10b-5p depletion severely impaired differentiation into mature adipocytes, as indicated by a lack of lipid droplet formation and reduced adipogenic gene expression. Gene expression analysis supports that miR-10b-5p directs embryonic stem (ES) cells towards the mesoderm lineage, promoting commitment to pre-adipocytes by downregulating Gata6 and its downstream target Bmp2. This mechanism appears to be unaffected in BAs. Our study demonstrated that miR-10b-5p regulates the later stages of adipogenesis, at least in part, by downregulating Tub, a direct target of miR-10b-5p. We also confirmed that miR-10b-5p alleviated the halted differentiation phenotypes of adipocytes by supressing the G Protein Signalling pathway mediated by Tubby. 2.4 Conclusions These results evidence that miR-10b inhibition plays a dynamic role in adipocyte biology, as its inhibitory effects manifest differently during the stem cell preadipocyte proliferation state and during the maturation phase of adipocytes. Collectively, our study demonstrated that miR-10b-5p may represent a new potential therapeutic target for lipodystrophy and obesity.

Abstract Background DOT1L, a histone H3 lysine 79 (H3K79) methyltransferase, is a potential therapeutic target in various malignancies. In the present study, we aimed to clarify the antitumor effect of DOT1L inhibition in breast cancer. Methods Estrogen receptor (ER)-positive/HER2-negative breast cancer cells (MCF7) and ER-negative/HER2-positive cells (SKBR3) were treated with a DOT1L inhibitor (SGC0942, EPZ-5676), after which colony formation assays, cell cycle assays, flow cytometry, gene expression microarray analysis, chromatin immunoprecipitation sequencing (ChIP-seq) and single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) were performed. Genetic ablation of STING was performed using the CRISPR/Cas9 system. Results Treatment with a DOT1L inhibitor suppressed proliferation and induced cell cycle arrest and apoptosis in both ER-positive/HER2-negative and ER-negative/HER2-positive cells. Transcriptome and epigenome analysis revealed that DOT1L inhibition activated transcription of a number of interferon (IFN)-related genes (IRGs) in breast cancer cells. We also found that DOT1L inhibition upregulated type I and type III IFNs and cell surface human leukocyte antigen (HLA) class I expression. Notably, DOT1L inhibition induced DNA damage and upregulated levels of cytoplasmic DNA in breast cancer cells. CRISPR/Cas9-mediated knockout of STING in breast cancer cells significantly suppressed the IFN signaling activated by DOT1L inhibition and attenuated the antitumor effects. Moreover, scATAC-seq analysis revealed that DOT1L inhibition suppressed expression of ERBB2 in HER2-positive breast cancer cells. Conclusions These findings suggest that the anti-breast cancer cell effects of DOT1L inhibition are mediated by multiple mechanisms, including activation of innate immune signaling.

Membrane protection against oxidative insults is achieved by the concerted action of glutathione peroxidase 4 (GPX4) and endogenous lipophilic antioxidants such as ubiquinone and vitamin E. Deficiencies in these protective systems lead to an increased propensity to phospholipid peroxidation and ferroptosis. More recently, ferroptosis suppressor protein 1 (FSP1) was identified as a critical ferroptosis inhibitor acting via regeneration of membrane-embedded antioxidants. Yet, regulators of FSP1 are largely uncharacterised, and their identification is essential for understanding the mechanisms buffering phospholipid peroxidation and ferroptosis. Here, we conducted a focused CRISPR-Cas9 screen to uncover factors influencing FSP1 function, identifying riboflavin (vitamin B₂) as a new modulator of ferroptosis sensitivity. We demonstrate that riboflavin, unlike other vitamins that act as radical-trapping antioxidants, supports FSP1 stability and the recycling of lipid-soluble antioxidants, thereby mitigating phospholipid peroxidation. Furthermore, we show that the riboflavin antimetabolite roseoflavin markedly impairs FSP1 function and sensitises cancer cells to ferroptosis. Thus, we uncover a direct and actionable role for riboflavin in maintaining membrane integrity by promoting membrane tolerance to lipid peroxidation. Our findings provide a rational strategy to modulate the FSP1-antioxidant recycling pathway and underscore the therapeutic potential of targeting riboflavin metabolism, with implications for understanding the interaction of nutrients and their contributions to a cell’s antioxidant capacity.

ABSTRACT Ferroptosis, a regulated form of cell death driven by excessive lipid peroxidation, has emerged as a promising therapeutic target in cancer. Ferroptosis suppressor protein 1 (FSP1) is a critical regulator of ferroptosis resistance, yet the mechanisms controlling its expression and stability remain mostly unexplored. To uncover regulators of FSP1 abundance, we conducted CRISPR-Cas9 screens utilizing a genome-edited, dual-fluorescent FSP1 reporter cell line, identifying both transcriptional and post-translational mechanisms that determine FSP1 levels. Notably, we identified riboflavin kinase (RFK) and FAD synthase (FLAD1), enzymes which are essential for synthesizing flavin adenine dinucleotide (FAD) from vitamin B2, as key contributors to FSP1 stability. Biochemical and cellular analyses revealed that FAD binding is critical for FSP1 activity. FAD deficiency, and mutations blocking FSP1-FAD binding, triggered FSP1 degradation via a ubiquitin-proteasome pathway that involves the E3 ligase RNF8. Unlike other vitamins that inhibit ferroptosis by scavenging radicals, vitamin B2 supports ferroptosis resistance through FAD cofactor binding, ensuring proper FSP1 stability and function. This study provides a rich resource detailing mechanisms that regulate FSP1 abundance and highlights a novel connection between vitamin B2 metabolism and ferroptosis resistance with implications for therapeutic strategies targeting FSP1 in cancer.

ABSTRACT Escherichia coli ( E. coli ) is a common bacterium in the human gut and an important cause of intestinal and extraintestinal infections. Some E. coli sequence types (ST) are associated with high pathogenicity. The Extraintestinal Pathogenic E. coli (ExPEC) ST131 is a globally distributed multidrug-resistant human pathogen associated with urinary tract and bloodstream infections. Antibiotic-resistant infections often lead to antibiotic treatment failure, underscoring the need of developing alternative treatments. The highly selective antimicrobial potential of CRISPR-Cas9 has been demonstrated in a range of model organisms. However, the effectiveness of CRISPR-Cas9 in combating ST131-associated infections and the consequences of CRISPR-Cas9 treatment, such as the emergence of escapers, remains unclear. Here, we investigated the antimicrobial activity of CRISPR-Cas9 against ST131 and assessed the frequency and genetic basis of escape. We conjugatively delivered CRISPR-Cas9 to ST131 isolates which carried cefotaxime-resistance-encoding target gene bla CTX-M-15 in the chromosome and characterized escape subpopulations. Two main types of escapers emerged: bla CTX-M-15 -positive escapers carried dysfunctional CRISPR-Cas9 systems and arose at a ∼10 −5 frequency. Instead, bla CTX-M-15 -negative escapers presented chromosomal deletions involving bla CTX-M-15 loss. The frequency of bla CTX-M-15 loss depended on the bla CTX-M-15 genetic context. Specifically, bla CTX-M-15 -negative escapers emerged at low frequency (∼10 −5 ) in isolates where bla CTX-M-15 was located downstream of insertion sequence (IS) IS Ecp1 , while escapers emerged with high frequency (∼10 −3 ) in isolates where bla CTX-M-15 was flanked by IS 26 . This work emphasizes how the genetic context of target genes can drive the outcome of CRISPR-Cas9 tools, where the presence of IS 26 may drive increased frequencies of escape. IMPORTANCE In the past decade CRISPR-Cas9 has emerged as an efficient antimicrobial tool capable of selective elimination of targeted bacteria. Even though it has been well described that bacteria can evolve to escape targeting by CRISPR-Cas9, the mechanisms of bacterial escape and their consequences remain largely elusive. In this study, we demonstrate the antimicrobial efficacy of CRISPR-Cas9 against natural isolates of Escherichia coli ST131, a clinically relevant pathogen, and elucidate the mechanism of escape from antimicrobial activity. We identify two distinct mechanisms of escape, which involve either dysfunctional CRISPR-Cas9 activity, or loss of the target gene ( bla CTX-M-15 ), with the latter occurring at frequencies that depend on the genetic context of the target gene. These findings provide important insights into the frequency and mechanisms of bacterial escape from CRISPR-Cas9-based antimicrobials and offer a foundation for the development of more effective treatments.

LMX1B, a LIM-homeodomain family transcription factor, plays critical roles in the development of multiple tissues, including limbs, eyes, kidneys, brain, and spinal cord. Mutations in the human LMX1B gene cause the rare autosomal-dominant disorder, Nail-patella syndrome which affects development of limbs, eyes, brain, and kidneys. In zebrafish, lmx1b has two paralogues: lmx1ba and lmx1bb. While lmx1b morpholino data exists, stable mutants were previously lacking. Here we describe the characterisation of lmx1b stable mutant lines, with a focus on development of tissues which are affected in Nail-patella syndrome. We demonstrate that the lmx1b paralogues have divergent developmental roles in zebrafish, with lmx1ba affecting skeletal and neuronal development, and lmx1bb affecting renal development. The double mutant, representing loss of both paralogues (lmx1b dKO) showed a stronger phenotype which included additional defects to trunk muscle patterning, and a failure to fully inflate the notochord leading to a dramatic reduction in body length. Overall, these mutant lines demonstrate the utility of zebrafish for modelling Nail-patella syndrome and describe a previously undescribed role for lmx1b in notochord cell inflation.