Abstract Heifer Infertility and disease are important challenges in dairy cattle production. Here, genetic differences between Holstein heifers with varying fertility potential and health were investigated. A genome-wide association analysis was carried out to compare heifers that conceived at first insemination against those requiring multiple attempts or failing to become pregnant, as well as heifers culled due to health issues. There were 12 significant SNPs (P<5x10 -5 ) associated with fertility and 35 SNPs associated with health traits. There were 166 significant SNPs when infertile, sub-fertile and animals culled due to health issues were grouped. Two SNPs identified in the analysis of infertility were found near NUFIP1 and within TENM4 genes, both genes are linked to embryonic lethality in mouse knockouts. Follow-up CRISPR-Cas9-mediated disruption of NUFIP1 significantly (P<0.05) reduced in vitro blastocyst development in cattle embryos, while TENM4 editing did not alter in vitro blastocyst development. Additionally, SNPs overlapped with previously identified reproduction-related QTL ( CNTN4 , DLG2 , PARP10 , PRICKLE , TMEM150B ) or health-related QTL ( FAM162A , PARP10 ). There were genes within or near genes previously associated with age at menarche ( CADM2, DLG2 , FHIT , LSAMP and TENM4 ) or lung function or pulmonary diseases ( ASCC2 , BCAS3 , BTBD9 , CADM2 , CNTN4 , CPEB4 , CTNNA2 , DEUP1 , DGKH , DLG2 , ENOX1 , EPHB1 , ERC2 , ERGIC1 , EYA2 , FAM162A , FGF18 , FHIT , GRID1, KCNIP4 , LINGO2 , LRMDA , MALRD1 , NEBL , PLA2G6 , PLXDC2 , PRPF18 , SLC8A1 , TEAD4 , TSPAN9 ) in humans. These results further support genetic components of fertility and health in cattle. The findings also show overlapping genetic architecture between heifer fertility and health traits, with a degree of conservation across mammals.

High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes; however, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here, we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR perturbations across the full spectrum of gene regulation, from chromatin remodeling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled over 300,000 cultured melanoma cells to characterize multi-modal phenotypic and gene regulatory responses to perturbations in more than 140 Vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent transcription factor (TF) activity signatures across diverse genetic perturbations. Combined inhibition of cooperative TF hubs effectively reversed cellular adaptation to Vemurafenib treatment. We further dissected phenotypic responses to perturbations in Mediator Complex components, linking module-specific biochemical properties to convergent gene activations. Together, we reveal common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineate how perturbations in functionally unrelated genes reshape cell state. PerturbFate thus establishes a versatile platform for identifying key molecular regulators by anchoring multi-modal regulatory dynamics to disease-relevant phenotypes.

Objective Catastrophic antiphospholipid syndrome (CAPS), characterized by widespread thrombosis and multi-organ failure, is associated with high morbidity and mortality. We previously established complement activation as a pathogenic driver of CAPS and identified rare germline variants in complement-regulatory genes including Complement Receptor 1 ( CR1 ) in 50% of CAPS. Methods We quantified CR1 expression by flow cytometry across hematopoietic cell types. CRISPR/Cas9 genome editing of TF-1 (erythroleukemia) cells was performed to generate CR1 “knock-out” and “knock-in” lines with patient-specific CR1 variants. Multiomics analysis was performed to investigate the role of methylation in CR1 expression in patients with reduced CR1 expression. Functional impact of low CR1 expression was assessed by complement-mediated cell killing using modified Ham (mHam) assay, cell-bound complement degradation products through flow cytometry and circulatory immune complexes (CIC) in serum samples through ELISA. Results CR1 expression in erythrocytes was markedly reduced on CAPS erythrocytes (n=9, 21.80%) compared to healthy controls (HC; n=32, 82.40%), with promoter hypermethylation emerging as a plausible epigenetic mechanism for CR1 downregulation. A novel germline variant ( CR1- V2125L; rs202148801 ) mitigated CR1 expression and increased complement-mediated cell death of knock-in cell lines. Erythrocytes from the patient with the CR1- V2125L variant had low CR1 expression. Levels of CIC, which are bound and cleared by CR1 on erythrocytes, were higher in acute CAPS (n=3, 25.55 µg Eq/ml) than healthy controls (n=3, 7.445 µg Eq/ml). Five patients were treated with C5 inhibition which mitigated thrombosis. Conclusion Genetic or epigenetic-mediated CR1 deficiency is a potential hallmark of CAPS and predicts response to C5 inhibition.

mRNA translation involves multiple regulatory steps, but how translation elongation in-fluences protein output remains unclear. Using SunTag live-cell imaging and mathematical modeling, we quantified translation dynamics in single mRNAs across diverse coding sequences. Our Totally Asymmetric Exclusion Process (TASEP)-based model revealed a strong coordination between initiation and elongation rates, resulting in consistently low ribosome density (≤12% occupancy) across all reporters. This coupling persisted under pharmacological inhibition of the elongation factor eIF5A, where proportional decreases in both initiation and elongation rates maintained homeostatic ribosome density. In contrast, eIF5A knockout cells exhibited a significant decrease in ribosome density, suggesting altered coordination. Together, these results highlight a dynamical coupling of initiation and elongation rates at the single-mRNA level, preventing ribosome crowding and maintaining translational homeostasis in mammalian cells.

Atrial fibrillation (AF) is a common arrhythmia with a complex genetic basis, yet the molecular mechanisms linking rare and common variants remain unclear. Using induced pluripotent stem cell-derived atrial cardiomyocytes, we uncover a novel mechanism by which a rare pathogenic LMNA variant encoding Lamin A/C disrupts chromatin accessibility and gene regulation at AF-associated loci. Specifically, reduced accessibility at an SCN5A enhancer harboring an AF-associated variant leads to reduced sodium current, conduction abnormalities, and re-entrant AF. These electrophysiological defects are rescued by CRISPR-mediated activation of the SCN5A promoter and enhancer, providing the first molecular evidence of epistatic gene-gene interactions driving arrhythmia risk and mechanistically linking atrial myopathy and AF. At the population level, we demonstrate that carriers of LMNA protein-altering variants with a high polygenic risk score are at a two-fold increased risk of early-onset AF, highlighting the need to integrate rare and common variants for more accurate AF risk assessment.

ABSTRACT Amyotrophic lateral sclerosis (ALS) caused by mutation in superoxide dismutase 1 ( SOD1 ) accounts for 15-30% of familial ALS and is typically autosomal dominant. How single base pair/amino acid changes in this small protein cause neurodegeneration is unknown. In North America, SOD1 A4V is the most common familial ALS SOD1 mutation and results in an aggressive form of ALS. Here, we present a novel genomically humanised mouse model of SOD1 A4V , in which the mouse Sod1 locus has been replaced by the human SOD1 gene, with intact genomic architecture of exons and introns, but bearing an A4V mutation. In agreement with previously reported human genomic knock-in mice, the phenotype is mild; however, transcriptomic and metabolomic profiling reveal significant dysregulation of glycolysis, the tricarboxylic acid (TCA) cycle, and lipid metabolism. These changes suggest an early bioenergetic imbalance that precedes neuromuscular impairment. Our findings support metabolic dysfunction as an early event in ALS pathogenesis. This freely available SOD1 A4V model provides a valuable tool for studying ALS progression and identifying therapeutic targets for pre-symptomatic treatment. SUMMARY STATEMENT This study describes the generation and analysis of novel genomically humanised SOD1 A4V mice, revealing metabolic dysfunction through integrated multi-omic analyses, characterising a freely available potential pre-symptomatic ALS model for future research.

ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor permissive genetic mutations, nature of cellular origin and microenvironmental stress. In this study, using primary human pancreatic acinar 3D organoids, we performed CRISPR knockout screen targeting 199 previously underappreciated potential tumor suppressors curated from clinical PDAC samples. Our data revealed significant enrichment of a list of candidates, with NF2 emerging as the top target. Functional validation confirmed that loss of NF2 promotes the transition of PDAC to an invasive state, potentially through extracellular matrix modulation. NF2 inactivation was found to enhance PDAC cell fitness under nutrient starvation. This adaptation not only reinforces the oncogenic state but also confers therapeutical resistance. Additionally, we found that NF2 loss is associated with the fibroblast heterogeneity and cancer-stroma communications in tumor evolution. These findings establish NF2 as a critical tumor suppressor in PDAC and uncover its role in mediating nutrient adaptation and drug resistance. Importantly, this study provides new insights into drug resistance mechanisms and potential therapeutic targets in PDAC.

The modification of mosquito populations at scale through CRISPR-Cas9-mediated homing gene drives is a promising route for malaria vector control. Integral gene drives (IGDs) are designed to utilize the regulatory sequences of endogenous genes to express only the minimal set of components required for gene drive. In this study, we describe the creation and characterization of the nanos d IGD targeting and inserted into the nanos gene of the malaria vector Anopheles gambiae and show that it achieves high rates of gene drive (97.7% in females, 99.0% in males). We find that homozygous nanos d females but not males show impaired fecundity, and a variable loss of ovary phenotype. Transcriptomic analysis of ovaries points to decreased transcript levels of the nanos gene when harbouring Cas9. As a minimal genetic modification, nanos d does not induce widespread transcriptomic perturbations, and its susceptibility to Plasmodium spp. and O’nyong nyong virus infection remains similar to wild-type mosquitoes. Importantly, we find that nanos d propagates efficiently in caged mosquito populations and is maintained as a source of Cas9 after the emergence of drive resistant alleles whilst also mobilising a non-autonomous antiparasitic effector modification. The nanos d gene drive shows promise as a genetic tool for malaria vector control via population modification, and we outline steps towards its further optimization.

CRISPR/Cas12a, recognized for its high efficiency and specificity in nucleic acid recognition, has found extensive applications in infectious disease sensing. Nonetheless, a significant challenge persists in devising a simple method for the rapid, convenient, and accurate visualization of detection results. In this study, we demonstrate an innovative and simple CRISPR-on-beads assay for visual detection of methicillin-resistant Staphylococcus aureus (MRSA). This approach combines isothermal target amplification, CRISPR/LbCas12a-mediated cleavage, and magnetic bead-based probe binding for signal amplification, enabling rapid and convenient identification of bacterial DNA. Our results show that this detection method exhibits both high sensitivity and specificity, with a detection limit as low as 30 CFU/μL. This newly developed biosensing approach can easily be integrated with a portable fluorescence microscope for medical diagnostics in resource-limited settings.

ABSTRACT Trypanosoma brucei , the causal agent of Human and Animal African trypanosomiasis proliferates in the extracellular milieu of mammals. It acquires host macromolecular nutrients, by receptor mediated endocytosis. The best characterised receptor is for transferrin (TfR) and it has been reported to be sequestered in the flagellar pocket, the sole site of endocytosis. In this location the TfR may be inaccessible to adaptive immune system effectors. The T. brucei genome encodes ∼15 TfR variants, and here we compared two, the first attached to the plasma membrane by a single glycosylphosphoinositol (GPI)-anchor and the other by two. Transferrin uptake kinetics were similar and rapid for both. Unexpectedly, initial binding of transferrin occurred over the whole cell surface suggesting the TfR was not sequestered in the flagellar pocket. This localisation was confirmed by immunofluorescence assays and was independent of the number of GPI-anchors. Two other GPI-anchored receptors were investigated to determine whether localisation to the whole cell surface was a general property of GPI-anchored receptors. Haptoglobin-haemoglobin uptake assays and immunofluorescence localisation of complement factor H receptor showed both were also whole cell surface localised. The mechanisms by which trypanosome receptors are protected from antibody-mediated attack are more subtle than hiding in a pocket.

Abstract Cytokinin signal transduction occurs through a "two-component system." Type-A and -C response regulators (RRs) are groups of proteins of similar structures constituting significant components of cytokinin signal transduction. In rice, 13 (Type-A) and two (Type–C) RRs have been identified to date; however, their functions remain partially known. In this study, we examined the expression patterns of Type-A and Type-C RRs in rice using RNA-Seq and confirmed their functions by constructing mutants of the 15 genes with CRISPR/Cas9. Almost all Type-A RRs played positive roles in the development of secondary branches and secondary spikelets, particularly RR2 and RR4 . Notably, rr1 rr2 and rr8 rr12 rr13 higher-order mutants displayed small panicle sizes and decreased plant height. Additionally, both Type-C RRs played positive roles in regulating heading date. RNA-seq revealed several genes with significantly altered expression in the rr2 and rr4 mutants, with almost half of the differentially expressed genes (DEGs) overlapping between the two mutants. Many of the DEGs were associated with the cytokinin and abscisic acid pathways.Our findings provide new insights into the functions of Type-A and -C RRs in rice growth and may serve as a foundation for future studies focusing on cytokinin signaling.

Abstract Background Cultivated tomato is susceptible to necrotrophic pathogens Botrytis cinerea and Alternaria solani . No dominant resistance against these pathogens has been reported in wild relatives of tomato. Results Through screening of a tomato Micro-Tom EMS population we identified a mutant that showed decreased susceptibility to both necrotrophic fungi. Previously, we reported a mutation in the tomato PUB17 gene as the cause of reduced susceptibility in this mutant. Surprisingly, M4 progeny of one M3 plant homozygous for the pub17 mutation showed segregation with some plants displaying an even higher level of resistance than the pub17 mutant. This highly resistant progeny was shown to contain a mutation in tomato PUB21 in addition to the mutation in PUB17 . The role of PUB21 as a susceptibility factor for both necrotrophic fungi was confirmed in RNAi-silenced and CRISPR-mutated transformants. Conclusions In this study we identified a new PUB gene, SlPUB21 , involved in susceptibility of tomato to necrotrophic pathogens. We showed that mutation of this gene resulted in increased resistance against these pathogens.

Abstract Archaeal antiviral defense systems remain poorly characterized despite recent advances in understanding prokaryotic immunity. Here, we analyze 7,747 archaeal genomes, the largest and most diverse dataset to date, revealing a striking disparity in defense system prevalence and diversity compared to Bacteria. Nearly one-third of archaeal genomes lack known systems beyond CRISPR-Cas and restriction-modification (in contrast to only 2.2% bacterial genomes), and only 31% contain CRISPR-Cas systems, far below previous estimates. While many known defense systems appear restricted to Bacteria, several single-gene candidate systems (PDCs) are enriched in Archaea. Phylogenetic analyses suggest that PDC-S27, PDC-S70, and PDC-M05 likely originated in Archaea, representing rare archaeal contributions to the prokaryotic immune repertoire. Consistent with earlier studies, our findings support the existence of deep evolutionary links between archaeal and eukaryotic systems for argonautes and viperins. These analyses highlight both the underexplored nature and the evolutionary significance of archaeal immunity, calling for expanded efforts to uncover archaeal-specific systems and improve our understanding of immune evolution across domains of life.

Bulk lipid transport between organelles has been proposed to involve the partnership between bridge lipid transport proteins and membrane-embedded lipid scramblases. However, for almost all BLTPs, such physical association has not been fully described, and, in most cases, the identity of the scramblases is unknown. Here, we identify TMEM170 family proteins as endoplasmic reticulum lipid scramblases that physically interact with BLTP1/Csf1 proteins. This finding opens new avenues to understand the complex mechanism involved in lipid transport at membrane contact sites.

Immune checkpoint inhibitor (ICB) therapy for many cancers remains limited in patients’ overall response rate. Discovery and development of more effective combinatorial approaches is urgent. Here, through CRISPR/Cas9 genetic screens, we identify DOT1L as a versatile epigenetic factor that functions to suppress tumor-intrinsic immunity through a dual mechanism. Depletion of DOT1L induces the expression of transposable elements and subsequent type I interferon (IFN) response, and meanwhile lowers ZEB1 levels to further unleash the expression of immune-related genes. In turn, we demonstrate that DOT1L loss or treatment with the clinical stage inhibitor EPZ-5676 sensitizes tumors to ICB with increased immune infiltration in mice. More importantly, EPZ-5676 treatment alone is sufficient to enhance antitumor immunity in humanized mice. TCGA data analysis reveals an inverse correlation between DOT1L expression and IFN signatures across multiple cancer types. These findings provide a rationale for targeting DOT1L to improve tumor immunogenicity and overcome immunotherapy resistance. One Sentence Summary CRISPR genetic screens identified DOT1L as a potential suppressor of tumor intrinsic immunogenicity

Objective The accumulation of DNA damage and mutations is a key contributor to aging. Recent studies have shown that disrupting the Beclin 1-BCL2 autophagy regulatory complex through gene editing can extend lifespan in mice. The precise application of gene editing technologies offers a promising strategy for aging. This study conducted a bibliometric analysis to map the knowledge landscape of gene editing and aging. Methods We retrieved publications related to genome editing and aging from the Web of Science Core Collection, covering the period from 2015 to 2024. The data were analyzed using VOSviewer and R package Bibliometrix. These tools enabled us to identify the most productive researchers, journals, institutions, countries and visualized current trends, emerging research hotspots. Results A total of 982 publications on genome editing and aging were identified. The United States (n=285) and China (n=214) form a dual-core structure leading global output. Harvard University (n=116) emerged as the most prolific institution. Scientific Reports was the top-publishing journal, with 23 articles in 2024. ZHANG Y (n=12, citations=102, H-index=6) was identified as the most productive author. KIM E’s 2017 publication in Nature Communications (TC=494, TC/year=54.9, NTC=9.33) has had a significant and ongoing impact. The analysis indicates that future directions will include CRISPR optimization and AI-assisted genomic analysis. Conclusion This study presents the first comprehensive bibliometric analysis and visualization of the knowledge structure in gene editing and aging research up to 2024. It offers researchers a detailed overview of current developments, trends, and emerging frontiers in this rapidly evolving domain.

Neurons contribute to the complex interplay of signals that mediate heart development and homeostasis. Although a limited set of studies suggest that neuronal peptides impact vertebrate heart growth, the specific contributions of these peptides to cardiomyocyte progenitor differentiation or proliferation have not been elucidated. Here we show that the neuropeptide tachykinin along with canonical Wnt signaling regulate cardiomyocyte progenitor proliferation in the chordate model Ciona robusta . In C. robusta, the heart continues to grow throughout adulthood and classic histological studies indicate that a line of undifferentiated cells may serve as a reserve progenitor lineage. We found that this line of cardiomyocyte progenitors consists of distinct distal and midline populations. Distal progenitors divide asymmetrically to produce distal and midline daughters. Midline progenitors divide asymmetrically to produce myocardial precursors. Through single cell RNA sequencing (scRNA-seq) of adult C. robusta hearts, we delineated the cardiomyocyte progenitor expression profile. Based on this data we investigated the role of Wnt signaling in cardiomyocyte progenitor proliferation and found that canonical Wnt signaling is required to suppress excessive progenitor proliferation. The scRNA-seq data also identified a number of presumptive cardiac neural-like cells. Strikingly, we found that a subset of these neuronal cells appears to innervate the distal cardiomyocyte progenitors. Based on the expression of the tachykinin receptor in these neuronal cells, we blocked tachykinin signaling using pharmacological inhibitors and found that this drove reduced proliferation in the distal progenitor pool. Through targeted CRISPR-Cas9 knockdown we then demonstrated that both extrinsic tachykinin and intrinsic, cardiac tachykinin receptors are required for formation of the myocardial heart tube. This work provides valuable insights into how organisms may deploy neural signals to regulate organ growth in response to environmental or homeostatic inputs.

ABSTRACT Optogenetic tools – whose engineering requires a structural understanding of the target proteins – are attractive approaches for achieving endogenous gene regulation under minimally invasive conditions. To build an optogenetic system for controlling endogenous gene expression, we first identified Anti-CRISPR (Acr) proteins that can inhibit CRISPRa-mediated transcriptional activation in Drosophila . Next, we inserted optogenetic protein LOV2 in these Acrs, tested for their ability to optogenetically modulate endogenous gene upregulation (EnGup) through the CRISPRa-based flySAM system in Drosophila , and found that the photoswitchability of these prototypes was weak. Hence, we engineered an Acr-LOV2 fusion module with refined length of intrinsically disordered and ordered regions (IDR and IOR) and optimized LOV2. This optimized variant, whose application yielded new findings in vivo , was significantly more sensitive for EnGup under blue light than the prototypes. In short, not only does this work introduce the application of Acr proteins in an animal model, but it also provides insights for in vivo characterization of the IDR and the IOR of these small-sized proteins. Together, these findings establish a robust optogenetic toolbox for precise, light-sensitive endogenous gene regulation in Drosophila . Graphical abstract

The human skin microbiome is shaped by a complex interplay of host physiology, environmental exposure, and microbial interactions across domains of life. However, the relative contributions of host genetics and geography remain unresolved. Here, we present the first application of ultra-low coverage human genome imputation from skin metagenomic data, analysing 1,756 samples from multiple skin types and timepoints, with matched genotypes from 327 individuals across five countries. We also generate expanded Skin Microbial Genome Collection (eSMGC), comprising 675 prokaryotic, 12 fungal, 2,344 viral, and 4,935 plasmid genomes, correcting extensive false positives in existing references. Intercountry comparisons reveal that geography explains more microbiome variation than skin type, and that host genetics contributes previously uncharacterized structure—exemplified by distinct profiles in Chinese individuals. Genome-wide association analysis identifies 107 SNPs linked to 22 microbial taxa, including phages and plasmids, implicating host genes in skin structure, immunity, and lipid metabolism. Cutibacterium acnes and its phages exhibit geographic divergence and phage–host co-adaptation. Finally, host-infecting viruses, particularly papillomaviruses, are associated with elevated microbial diversity and immune-modulatory functions. These findings establish host genetics as a determinant of skin microbiome ecology and highlight the value of multi-domain, geographically diverse analyses.

Synthetic lethality describes a genetic relationship where the loss of two genes results in cell death, but the loss of one of those genes does not. Drugs used for precision oncology can exploit synthetic lethal relationships; the best described are PARP inhibitors which preferentially kill BRCA1 -deficient tumours preferentially over BRCA1 -proficient cells. New synthetic lethal targets are often discovered using genetic screens, such as CRISPR knockout screens. Here, we present a competitive co-culture assay that can be used to analyse drugs or gene knockouts with synthetic lethal effects. We generated new BRCA1 isogenic cell line pairs from both a triple-negative breast cancer cell line (SUM149) and adapted pre-existing non-cancerous BRCA1 isogenic pair (RPE). Each cell line of the isogenic pair was transformed with its own fluorescent reporter. The two-coloured cell lines of the isogenic pair were then grown together in the same vessel to create a more competitive environment compared to when grown separately. We used four PARP inhibitors to validate the ability to detect synthetic lethality in BRCA1 -deficient cancer cells. The readout of the assay was performed by counting the fluorescently coloured cells after drug treatment using flow cytometry. We observed preferential targeting of BRCA1- deficient cells, by PARPi, at relative concentrations that broadly reflect clinical dosing. Further we reveal subtle differences between PARPi resistant lines compared to BRCA1- proficient cells. Here, we demonstrate the validation and potential use of the competitive assay, which could be extended to validating novel genetic relationships and adapted for live cell imaging.

Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membrane recruitment. Here, we present a generalizable strategy for engineering thermosensitive allosteric proteins through the insertion of optimized Avena sativa LOV2 domain variants. Applying this approach to a diverse set of structurally and functionally unrelated proteins in Escherichia coli , we generated potent, thermo-switchable chimeric variants that can be tightly controlled within narrow temperature ranges (37-41°C). Extending this strategy to mammalian systems, we engineered the first CRISPR-Cas genome editors directly modulated by subtle temperature changes within the physiological range. Finally, we showcase the incorporation of a chemoreceptor domain as an alternative thermosensing module, suggesting thermo-sensitivity to be a widespread feature in receptor domains. This work expands the toolkit of thermogenetics, providing a blueprint for temperature-dependent control of virtually any protein of interest.

ABSTRACT Lentiviral vectors are a cornerstone delivery modality of biomedical research, renowned for their ability to stably integrate genetic material into the host genome, enabling sustained transgene expression and long-term genetic manipulation. These properties make them indispensable tools in functional genomics and genome engineering, particularly for delivering molecular components in high-throughput CRISPR screening, a powerful approach for uncovering the genetic basis of complex cellular mechanisms and phenotypes. However, challenges such as lentiviral-induced recombination, unpredictable integration profiles, and variable susceptibility of target cells to transduction can introduce noise and compromise experimental outcomes. In this study, we selected two suspension-adapted mammalian cell lines, Chinese Hamster Ovary cells CHO-K1 and Human Embryonic Kidney cells HEK293-6E, due to their widespread use in recombinant protein production. Recognizing the influence of intrinsic cell line properties and transduction methodology, we compared two distinct procedures: spinoculation and static transduction. By implementing a two-step static transduction protocol, we achieved significantly higher transduction efficiencies while minimizing cellular stress, streamlining workflows, and eliminating scalability limitations inherent to large-scale lentiviral applications like genome-wide CRISPR screens. To further characterize the variation in lentiviral integration, we used droplet digital PCR (ddPCR) to quantify copy number variation (CNV) both at the pooled population level and within individual clonal isolates. This comprehensive analysis underscores the robustness of our optimized protocol in enhancing transduction efficiency in difficult-to-transduce suspension cell lines. It further emphasizes the importance of carefully modulating infection rates to limit multiple integrations, ensuring the accuracy and consistency required for large-scale functional genomics applications.

ABSTRACT Ethanol is a fermentation product widely used as a fuel and chemical precursor in various applications. However, its accumulation imposes severe stress on the microbial producer, leading to significant production losses. To address this, improving a strain’s ethanol tolerance is considered an effective strategy to enhance production. In our previous research, we conducted an adaptive evolution experiment with Escherichia coli growing under gradually increasing concentrations of ethanol, which gave rise to multiple hypertolerant populations. Based on the genomic mutational data, we demonstrated in this work that adaptive alleles in the EnvZ-OmpR two-component system drive the development of ethanol tolerance in E. coli . Specifically, when a single leucine was substituted for a proline residue within the periplasmic domain using CRISPR, the mutated EnvZ osmosensor caused a significant increase in ethanol tolerance. Through promoter fusion assays, we showed that this particular mutation stabilizes EnvZ in a kinase-dominating state, which reprograms signal transduction involving its cognate OmpR response regulator. Whole-genome proteomics analysis revealed that this altered signaling pathway predominantly maintains outer membrane stability by upregulating global porin levels and attenuating iron metabolism in the tolerant envZ* L116P mutant. Moreover, we demonstrated that the hypertolerant envZ* L116P allele also promotes ethanol productivity in fermentation, providing valuable insights for enhancing industrial ethanol production. AUTHOR SUMMARY Ethanol is a versatile chemical with many applications, but producing it in high quantities remains a challenge. This is because Escherichia coli , a candidate ethanol production strain, is naturally sensitive to this short-chain alcohol, especially when levels are gradually accumulating during fermentation. To resolve this bottleneck, we have investigated how E. coli can acquire tolerance to its own toxic fermentation product. Our research indicated that a single amino acid substitution in EnvZ-a key sensor protein that normally protects E. coli against extreme osmotic stress-is sufficient to confer ethanol tolerance. Further analysis revealed that the mutation perturbs the EnvZ-mediated signaling cascade, which, in turn, changes the transporter composition in the outer membrane and attenuates the cell’s iron metabolism. These adaptations enable E. coli to survive under high-ethanol conditions, thereby promoting its ethanol production efficiency. This discovery provides a suitable strategy to increase ethanol titers in industrial settings using fermentation.

Background Metastatic colorectal cancer (mCRC) is associated with high recurrence rates and resistance to conventional treatments, largely driven by cancer stem cells (CSCs) that contribute to tumor progression and therapeutic evasion. This study aims to investigate the role of netrin-1 and its dependence receptor UNC5B in regulating CSC self-renewal in mCRC and explore their potential as therapeutic targets. Methods We used patient-derived liver metastasis organoids (PDOs) to examine the effects of netrin-1 on CSC self-renewal. The role of UNC5B was evaluated by silencing its expression using CRISPR and assessing the impact on CSC apoptosis in response to an anti-netrin-1 blocking antibody (NP137) using extreme limiting dilution assays (ELDAs). Single-cell RNA sequencing was employed to explore the molecular mechanisms behind netrin-1/UNC5B regulation of CSC fate. Clinical data from a patient with mCRC were used to validate the findings. Results Netrin-1 promoted CSC self-renewal by inhibiting apoptosis, a process reversed by NP137. UNC5B was identified as the primary receptor mediating this effect, as its silencing eliminated Netrin-1-induced self-renewal. Trefoil Factor 3 (TFF3), secreted by UNC5B-expressing cells, plays a key role in netrin-1-induced CSC self-renewal. Clinical trial data from a patient with mCRC showed a reduction in TFF3 and stemness genes expression after treatment with NP137. Furthermore, combining NP137 with FOLFOX chemotherapy enhanced cell death and inhibited tumor growth in PDO xenograft models. Conclusion This study identifies the netrin-1/UNC5B/TFF3 axis as a critical regulator of CSC self-renewal in mCRC and suggests that targeting this pathway with NP137, in combination with chemotherapy, could provide a promising therapeutic approach for mCRC patients.

Despite major advances in genetic screening technology, a formal approach for quantifying gene function remains underdeveloped, thereby limiting the utility of these techniques in deciphering the complex behavior of human cells. In this study, we leverage information theory with a perturbational analysis of replicator dynamics to characterize functional drivers of selection in pooled CRISPR screens. Our approach challenges established methods for CRISPR screen analysis, while offering additional insight into selection dynamics through the Kullback-Leibler divergence ( D KL ) and cumulants of the fitness distribution. By modeling fluctuations in gene-fitness effects as a linear response to environmental perturbations, we derive a geometric measure for genomic information content based on a second-order approximation of the D KL . Our analysis reveals that functional information—encoded (or shared) between genes—can be quantified by analyzing the directions corresponding to maximal conditional selection within the space of decomposed gene-environment interactions. This geometric representation offers several advantages for the functional analysis of the human genome and its network architecture. Moreover, by constraining the space to cell-type-specific fluctuations, we uncover developmental and tissue-specific functional signatures. These findings represent significant progress in the dynamic analysis of gene function and in the functional wiring of the human genome.