RNA therapeutics are emerging as transformative modalities in clinical applications and have become a key area in life science research. While lipid nanoparticles (LNPs) have become the leading platform for RNA delivery in preventive and therapeutic products, they still face significant challenges in achieving efficient extrahepatic delivery and maintaining long term shelf stability. Here we report the development of a series of biodegradable poly( β -amino amide) (PBAA) polymers, detailing their design, synthesis, and performance as gene delivery vehicles both in vitro and in vivo . These cationic polymers, featuring interspersed trialkylamine motifs, provide a readily tunable functional handle and facilitate complexation with gene cargo. The redox-sensitive disulfide motifs introduce a redox-responsive decomposition pathway for the polymer backbone, triggering cargo release during intracellular delivery. The results herein demonstrate that these polymers offer remarkable efficiency in encapsulating and delivering translation-competent cargos, including mRNA and CRISPR-Cas based gene editing tools. Notably, a dodecyl modified PBAA transporter has achieved over 97% gene editing efficiency in vitro , and over 97% spleen-targeting selectivity in a murine model. Additionally, it produces stable nanoparticles that maintain their physicochemical properties at 4 °C for up to two weeks without addition of excipients such as PEG, offering a cost-effective solution for RNA therapeutics supply chains. As the transformative impact of RNA and other nucleic acids continues to build within the pharmaceutical industry and beyond, it is imperative that the supporting technologies evolve in stride to maximize said impact. The tunable and biodegradable PBAA polymer designs presented herein are illustrative examples of how high-level functional performance can be acheived in conjunction with the critical targeting, formulation, and operational simplicity needed of state-of-the-art transfection and delivery technologies.

Bacillus thuringiensis is widely employed for biological control. It can effectively suppress populations of various mosquito species, including Aedes aegypti . However, the precise mechanism underlying the action of cry toxin secreted by Bacillus thuringiensis on Ae. aegypti remains elusive. In this study, we investigated one of the binding receptors of cry toxin, aminopeptidase N. Through comprehensive bioinformatics analysis involving whole-genome screening, genetic mapping, structural characterization, phylogenetic analysis, and spatiotemporal expression profiling, we identified twenty-nine homologs of Ae. aegypti aminopeptidase N. Further, we successfully expressed GST-APN3 protein in E. coli and demonstrated through ligand blot and ELISA assays that APN3 exhibits high affinity binding to Cry4Ba toxin (Kd = 20.53 nM). To elucidate the functional role of APN3 as a receptor mediating Cry4Ba activity in Ae. aegypti midgut cells (some of which express this gene at high levels), CRISPR/Cas9 technology was employed to knock out APN3. Our bioassay results revealed that APN3 knockout mosquito larvae had 2.9 to 4.1-fold higher resistance against Cry4Ba, indicating its crucial involvement as an active receptor mediating Cry4Ba activity. Overall, this study provides a foundation for elucidating the specific larvicidal mechanisms of Bt against mosquito populations.

Background Endozoicomonas is a widely distributed genus of marine bacteria, associated with various marine organisms, and recognized for its ecological importance in host health, nutrient cycling, and disease dynamics. Despite its significance, genomic features of Endozoicomonas remain poorly characterized due to limited availability of high-quality genome assemblies. Results In this study, we sequenced 5 novel Endozoicomonas strains and re-sequenced 1 known strain to improve genomic resolution. By integrating these 6 high-quality genomes with 31 others that were publicly available, we identified a distinct, coral-associated clade not recognized by the previous two-clade classification. Pan-genomic analysis revealed significant variation in genetic trait distribution among clades. Notably, Endozoicomonas lacks quorum sensing capabilities, suggesting resistance to quorum quenching mechanisms. It also lacks the ability to synthesize and transport vitamin B12, indicating that it is not a primary source of this nutrient for holobionts. A remarkable feature of Endozoicomonas is its abundance of giant proteins, ranging from 15 to 65 kbp. We identified 92 such proteins, which clustered into three major groups based on amino acid similarity, each associated with specialized functions, such as antimicrobial synthesis, exotoxin production, and cell adhesion. Additionally, we explored prophages and CRISPR-Cas systems. We found that Endozoicomonas acquired prophages from diverse sources via infection or other types of gene transfer. Notably, CRISPR-Cas sequences suggest independent evolutionary trajectories from both prophage acquisition and phylogenetic lineage, implying a potential influence of geographic or environmental pressures. Conclusions This study provides new insights into the genomic diversity of Endozoicomonas and its genetic adaptation to diverse hosts. Identification of novel genomic features, including deficiencies in B12 synthesis and quorum sensing, the presence of giant proteins, prophages, and CRISPR-Cas systems, underscores its ecological roles in various holobionts. These findings open new avenues for research on Endozoicomonas and its ecological interactions.

Heart failure (HF) is a global health challenge characterized by the heart’s inability to satisfy metabolic demands, driven by renin-angiotensin-aldosterone system (RAAS) overactivation, neurohormonal imbalance, and emerging mechanisms like the gut-heart axis and mitochondrial dysfunction. Affecting over 6 million adults in the US alone, HF incurs a 5-year mortality rate of 50% and escalating costs projected to double by 2030. This review examines HF’s molecular paradigms, integrating established pathways with advances in omics, stem cell therapy, genetic modification, and personalized medicine. RAAS blockade remains central, yet its efficacy is limited in HF with preserved ejection fraction (HFpEF). Stem cell therapies (mesenchymal and induced pluripotent stem cells) show regenerative potential but face poor retention (10% survival at 30 days). CRISPR/Cas9 offers precision, though off-target effects persist. The gut microbiome, via trimethylamine N-oxide, exacerbates inflammation, while omics technologies promise biomarkers for tailored treatments. Challenges include translating these innovations into practice, particularly for HFpEF. Future directions involve novel HFpEF therapies, enhanced stem cell delivery, precise genetic tools, and microbiome interventions, supported by artificial intelligence. By 2030, these advances could shift HF management toward regeneration, contingent on overcoming translational barriers through global collaboration.

ABSTRACT Background Current lipid-lowering drugs reduce low-density lipoprotein (LDL) cholesterol by enhancing the LDL receptor (LDLR) pathway and are relatively ineffective in patients with Familial Hypercholesterolemia (FH) due to a dysfunctional LDLR. Angiopoietin-like 3 (ANGPTL3) inhibitors reduce LDL cholesterol in FH patients through an uncharacterized, LDLR-independent pathway that requires endothelial lipase (EL). Kinetic studies in FH patients showed that ANGPTL3 inhibitors directly enhanced LDL catabolism; however, EL’s role in this pathway remains unclear. Here, we aim to investigate the mechanisms by which EL mediates LDLR-independent uptake of LDL in hepatocytes. Methods CRISPR/Cas9-generated control and LDLR-KO HepG2 cells were transfected with an empty plasmid or a plasmid encoding the human LIPG gene, and the cellular uptake of fluorescent human LDL was measured by FACS. Additionally, to test the contribution of heparan sulfate proteoglycans (HSPG), cellular LDL uptake was assessed with and without the pre-incubation with heparin or a cocktail of heparinases. Finally, LDL uptake was measured after incubating cells with tetrahydrolipstatin (THL) to inhibit EL enzymatic activity. Results As expected, LDLR-KO HepG2 cells showed an 80% reduction in LDL uptake compared to controls (p<0.001). Remarkably, EL overexpression almost fully rescued LDL uptake in LDLR-KO cells (p<0.001), while no effect was observed in control cells. EL-mediated LDL uptake was completely blocked by heparinases and heparin in LDLR-KO cells, suggesting a crucial role of HSPG in the EL-mediated LDL uptake. Notably, treatment with THL reduced the cellular LDL uptake in LDLR-KO cells overexpressing EL (p=0.0015). Conclusions EL facilitates the uptake of LDL in hepatocytes through an LDLR-independent, HSPG-dependent pathway that involves EL activity. Our data provides an alternative mechanism to explain the reduction of LDL cholesterol induced by ANGPTL3 inhibitors. This pathway represents a potential druggable target to treat FH.

Mycobacterium abscessus (Mab) causes pulmonary diseases with limited treatment options due to its high level of intrinsic resistance to available drugs. Mab possesses complex and poorly understood drug resistance mechanisms. Identifying new drug targets and gaining a deeper understanding of drug resistance mechanisms are essential for discovering novel therapeutic alternatives. Here, we investigated the role of a putative sigma factor SigH in intrinsic multi-drug resistance in Mab. Mab SigH shares an 84% peptide sequence identity with Mycobacterium tuberculosis (Mtb) SigH, a well-known stress response protein and global transcriptional regulator. We constructed a sigH gene deletion strain of Mab (Δ sigH ) and complemented strains by expressing either Mab sigH (CPMab sigH ) or Mtb sigH (CPMtb sigH ) in Δ sigH. The Δ sigH strain exhibited hypersensitivity to a broad range of antibiotics, including levofloxacin, moxifloxacin, tigecycline, tetracycline, amikacin, vancomycin, and rifabutin and all complemented strains restored the drug resistance phenotype. Additionally, Δ sigH showed increased sensitivity to oxidative and heat stress compared to the wild-type Mab and complemented strains. Transcriptomic analysis revealed that deletion of sigH disrupted the balance of gene expression, primarily elevating the expression of genes encoding YrbE and MCE family proteins and downregulating genes expressing ABC-type transporters, sigma and anti-sigma factors and other genes associated with antimicrobial resistance. Collectively, our findings indicate that SigH is a key regulator of global gene expression in response to environmental stresses, including antimicrobial treatment, and is crucial for the intrinsic drug resistance of Mab. SigH represents a promising target for the development of novel therapeutic strategies against Mab infections.

Lipid nanoparticle (LNP)-based mRNA therapeutics, highlighted by the success of SARS-CoV-2 vaccines, face challenges due to inflammation caused by ionizable lipids. These ionizable lipids can activate the immune system, particularly when co-delivered with nucleic acids, leading to undesirable inflammatory responses. We introduce a novel class of anti-inflammatory ionizable lipids functionalized with hydroxychloroquine (HCQ), which suppresses both lipid-induced and nucleic acid-induced immune activation. These HCQ-functionalized LNPs (HL LNPs) exhibit reduced proinflammatory responses while maintaining efficient mRNA delivery. Structural and physicochemical analyses revealed that HCQ-functionalization results in a distinct particle structure with significantly improved stability. The efficacy of HL LNPs was demonstrated across various therapeutic contexts, including a prophylactic vaccination model against varicella-zoster virus (VZV) and CRISPR-Cas9 gene editing targeting PCSK9. Notably, HL LNPs showed robust mRNA expression after repeated administration, addressing concerns of inflammation and ensuring sustained therapeutic effects. These findings highlight the potential of HCQ-functionalized LNPs in expanding the safe use of mRNA therapeutics, particularly for applications requiring repeated dosing and in scenarios where inflammation-induced side effects must be minimized.

Streptomyces bacteria make diverse specialised metabolites that form the basis of ∼55% of clinically used antibiotics. Despite this, only 3% of their encoded specialised metabolites have been matched to molecules and understanding how their biosynthesis is controlled is essential to fully exploit their potential. Here we use Streptomyces formicae and the formicamycin biosynthetic pathway as a model to understand the complex regulation of specialised metabolism. We analysed all three pathway-specific regulators and found that biosynthesis is subject to negative feedback and redox control via two MarR-family proteins while activation of the pathway is dependent on a cytoplasmic two-component system. Like many Streptomyces antibiotics, formicamycins are only produced in solid culture and biosynthesis is switched off in aerated liquid cultures. Here, we demonstrate that a redox-sensitive repressor named ForJ senses oxygen via a single cysteine residue that is required to repress formicamycin biosynthesis in liquid cultures.

CRISPR-associated transposons (CAST) consist of an integration between certain class 1 or class 2 CRISPR-Cas systems and Tn7-like transposons. Class 2 type V-K CAST systems are restricted to cyanobacteria. Here, we identified a unique subgroup of type V-K systems through phylogenetic analysis, classified as V-K_V2. Subgroup V-K_V2 CAST systems are characterized by an alternative tracrRNA, the exclusive use of Arc_2-type transcriptional regulators, and distinct differences in TnsB and TnsC proteins. Although the occurrence of V-K_V2 CAST systems is restricted to Nostocales cyanobacteria, it shows signs of horizontal gene transfer, indicating its capability for genetic mobility. The predicted V-K_V2 tracrRNA secondary structure has been integrated into an updated version of the CRISPRtracrRNA program available on GitHub under https://github.com/BackofenLab/CRISPRtracrRNA/releases/tag/2.0 .

Abstract The accumulation of misfolded protein species underlies a broad range of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Due to their dynamic nature, these misfolded proteins have proven challenging to target therapeutically. Here, we specifically target misfolded disease variants of the ALS-associated protein; SOD1, using a biological proteolysis targeting chimera (BioPROTAC) composed of a SOD1-specific intrabody and an E3 ubiquitin ligase. Screening of intrabodies and E3 ligases for optimal BioPROTAC construction revealed a candidate capable of degrading multiple disease variants of SOD1, preventing their aggregation in cultured cells. Using CRISPR/Cas9 technology to develop a BioPROTAC transgenic mouse line, we demonstrate that the presence of the BioPROTAC delays disease progression in the SOD1G93A mouse model of ALS. Delayed disease progression was associated with protection of motor neurons, reduced accumulation of insoluble SOD1 and protection of neuromuscular junctions. These findings provide proof-of-concept evidence and a platform for developing BioPROTACs as a therapeutic strategy for the targeted degradation of neurotoxic misfolded species in the context of neurodegenerative diseases.

Hypophosphatasia (HPP) is a rare inborn error of metabolism caused by pathogenic var-iants in ALPL, coding for tissue non-specific alkaline phosphatase. HPP patients suffer from impaired bone mineralization and in severe cases from vitamin B6-responsive sei-zures. To study HPP we generated alpl-/- zebrafish line using CRISPR/Cas9 gene-editing technology. At 5 days post fertilization (dpf) no alpl mRNA and 89% lower total alkaline phosphatase activity was detected in alpl-/- compared to alpl+/+ embryos. The survival of alpl-/- zebrafish was strongly decreased. Alizarin red staining showed decreased bone mineralization in alpl-/- embryos. B6 vitamer analysis revealed depletion of pyridoxal and its degradation product 4-pyridoxic acid in alpl-/- embryos. Accumulation of d3-pyridoxal 5’-phosphate (d3-PLP) and reduced formation of d3-pyridoxal in alpl-/- embryos incu-bated with d3-PLP confirmed Alpl involvement in vitamin B6 metabolism. Locomotion analysis showed pyridoxine treatment-responsive spontaneous seizures in alpl-/- embryos. Metabolic profiling of alpl-/- larvae using direct-infusion high-resolution mass spectrome-try showed abnormalities in polyamine and neurotransmitter metabolism, suggesting dysfunction of vitamin B6-dependent enzymes. Accumulation of N-methylethanolaminium phosphate indicated abnormalities in phosphoethanolamine metabolism. Taken together, we generated first zebrafish model of HPP that shows multi-ple features of human disease and is suitable to study pathophysiology of HPP and to test novel treatments.

Intratumor transcriptional heterogeneity (ITTH) presents a major challenge in cancer treatment, particularly due to limited understanding of the diverse malignant cell populations and their relationship to therapy resistance. While single-cell sequencing has provided valuable insights into tumor composition, its high cost and technical complexity limits its use for large-scale tumor screening. In contrast, several databases collecting bulk RNA sequencing (RNA-seq) data from multiple samples across various cancer types are available and could be used to profile ITTH. Several deconvolution approaches have been developed to infer cellular composition from such data. However, most of these methods rely on predefined markers or single cell reference datasets, limiting the performance of such methods by the quality of used reference data. Although unsupervised approaches do not face such limitations, existing methods have not been specifically adapted to characterize malignant cell states, and focus instead on general cell types. To address these gaps, we introduce CDState, an unsupervised method for inferring malignant cell subpopulations from bulk RNA-seq data. CDState utilizes a Nonnegative Matrix Factorization model improved with sum-to-one constraints and a cosine similarity-based optimization to deconvolve bulk gene expression into distinct cell state-specific profiles, and estimate the abundance of each state across tumor samples. We validate CDState using bulkified single-cell RNA-seq data from five cancer types, showing that it outperforms existing unsupervised deconvolution methods in both cell state proportions and gene expression estimation. Applying CDState to 33 cancer types from TCGA, we identified recurrent malignant cell programs, with epithelial-mesenchymal transition as the main driver of tumor transcriptional heterogeneity. We further link the identified malignant states to patient clinical features, revealing states associated with worse patient prognosis. We show that ITTH is linked with patient survival and clinical features, as well as is associated with varied responses to therapy. Finally, we identified potential genetic drivers of ITTH and malignant cell states, including TP53 , KRAS , and PIK3CA , known oncogenic genes.

Cis-regulatory elements (CREs) control how genes respond to external signals, but the principles governing their structure and function remain poorly understood. While differential transcription factor binding is known to regulate gene expression, how CREs integrate the amount and combination of inputs to secure precise spatiotemporal profiles of gene expression remains unclear. Here, we developed a high-throughput combinatorial screening strategy, that we term NeMECiS, to investigate signal- dependent synthetic CREs (synCREs) in differentiating mammalian stem cells. By concatenating fragments of functional CREs from genes that respond to Sonic Hedgehog in the developing vertebrate neural tube, we found that CRE activity follows hierarchical design rules. While individual 200-base-pair fragments showed minimal activity, their combinations generated thousands of functional signal-responsive synCREs, many exceeding the activity of natural sequences. Statistical modelling revealed CRE function can be decomposed into specific quantitative contributions in which sequence fragments combine through a multiplicative rule, tuned by their relative positioning and spacing. These findings provide a predictive framework for CRE redesign, which we used to engineer synthetic CREs that alter the pattern of motor neuron differentiation in neural tissue. These findings establish quantitative principles for engineering synthetic regulatory elements with programmable signal responses to rewire genetic circuits and control stem cell differentiation, providing a basis for understanding developmental gene regulation and designing therapeutic gene expression systems.

We established a novel knock-in technique, New and Easy Xenopus Targeted integration ( NEXTi ), to recapitulate endogenous gene expression by reporter expression. NEXTi is a CRISPR-Cas9-based method to integrate a donor DNA containing a reporter gene ( egfp ) into target 5’ untranslated region (UTR) of Xenopus laevis genome. It enables us to track eGFP expression under regulation of endogenous promoter/enhancer activities. We obtained about 2% to 13% of knock-in vector-injected embryos showing eGFP signal in a tissue-specific manner, targeting krt.12.2.L , myod1.S , sox2.L and bcan.S loci, as previously reported. In addition, F1 embryos which show stable eGFP signals were obtained by outcrossing the matured injected frogs with wild-type animals. Integrations of donor DNAs into target 5’ UTRs were confirmed by PCR amplification and sequencing. Here, we describe the step-by-step protocol for preparation of donor DNA and single guide RNA, microinjection and genotyping of F1 animals for the NEXTi procedure. 1. Highlight Intended organism: Xenopus laevis Purpose: of the protocol: Efficient knock-in for visualizing endogenous target gene expression using CRISPR-Cas9 system Essential equipment and materials: Microinjector, fluorescence microscopy, Cas9 protein, sgRNA, donor DNA Features: Expression of reporter genes depends on endogenous enhancer/promoter activities.

Hypoxia, a hallmark of solid tumors, promotes the malignant progression and is challenging to target. Metabolic reprogramming and the resulting metabolic vulnerabilities provide a promising strategy to target tumor hypoxia. Here we systematically compared the metabolic network differences between hypoxic and non-hypoxic cells, and developed a deep learning model, “DepFormer”, to predict the dependent metabolic genes in hypoxic tumor cells. The performance of DepFormer was validated using CRISPR screening dataset. Oxidative phosphorylation was identified as the most significantly hypoxia-dependent metabolic pathway, and FLAD1 was predicted to be one of the key hypoxia-dependent metabolic genes. FLAD1 locus is amplified, and FLAD1 expression is upregulated in various tumor types, especially in hypoxic tumors. FLAD1 depletion compromises tumor’s adaptation to hypoxia by disrupting mitochondrial complex II activity, leading to an imbalance between succinate and fumarate, and consequent failure to adapt to hypoxia. Subsequently, we identified a drug-like inhibitor of FLAD1, which selectively inhibits the growth of tumor cells under hypoxia. Our findings reveal FLAD1 as an innovative therapeutic target for hypoxic tumors.

Soybean transformation remains challenging and has not kept pace with the rapid advancement of genetic engineering technologies due to low efficiency, lengthy timelines, and genotype dependency. Here, we developed a streamlined transformation method by leveraging developmental regulators (DRs) to promote de novo shoot regeneration directly from growing soybean plants. By evaluating multiple DR combinations, our results showed that co-expression of WUSCHEL2 ( WUS2 ) and isopentenyltransferase ( IPT ) achieved higher transformation efficiencies (15.2% to 22.3%) in Williams 82 and Bert varieties than individual DRs without requiring exogenous hormones or selection agents. Moreover, this method produces heritable transgenic events within 9-11 weeks and successfully delivers CRISPR-Cas9 components, generating heritable mutations with 20% efficiency. The temporal transcriptomic and gene regulatory network analyses revealed that WUS2 / IPT synergistically modulates stress responses and activates developmental pathways, orchestrating a transition from initial stress adaptation to regenerative programming. Together, our findings demonstrate that this DR-enabled approach significantly enhances soybean transformation efficiency, reduces tissue culture requirements, and offers a promising genome editing platform for soybean improvement.

Background Calcific aortic valve stenosis (AS) affects 3% of older adults and lacks medical treatment. The deacetylase Sirtuin 1 (SIRT1) could be involved in many pathways linked to AS progression. Sodium-glucose co-transporter 2 inhibitors (SGLT2i), glucose-lowering agents, have been shown to reduce cardiovascular events (likely via SIRT1), but their possible benefits in AS are unknown. Our study aims to uncover the role of SIRT1 in AS progression and assess the benefit of SGLT2i to slow down the aortic valve fibro-calcification processes. Methods RNA-seq data of human aortic valve specimens were collected from ARChS4 database. SIRT1 knockdown (SIRT1 KD) and overexpressing (SIRT1 Over) valve interstitial cells (VIC) were generated by CRISPR/Cas9. Real-time PCR, immunofluorescence, and calcification assays were used to characterized mutant VICs. Conditioned medium experiments were implemented to evaluate SGLT2i effect on cellular cross-talk and calcification. Diabetic patients’ data from the Lombardy regional healthcare database, treated with sulphonylureas (SU; no effect on SIRT1) and SGLT2i (acting on SIRT1), were selected and matched 1:1 by age, sex, and multisource comorbidity score. Cumulative incidence of hospitalization for non-rheumatic aortic valve disease was assessed by Kaplan-Meier and multivariable Cox proportional hazards models were used to estimate hazard ratios. Results RNA-seq showed that SIRT1 could be a master regulator of multiple AS-related pathways. Functional studies on mutant VICs revealed that SIRT1 directly regulates antioxidant processes, extracellular-matrix remodeling and calcification by modulating key transcription factors. Moreover, calcification assays further support this role, revealing an increased calcification in SIRT1 KD VICs and a concomitant decrease in VIC SIRT1 Over when compared to wild type. Then, exploring SGLT2i impact on calcification, we showed that VICs cultured in SGLT2i-treated-endothelial medium exhibited reduced calcification associated with endothelial-increased nitric oxide levels, while SIRT1 inhibition enhanced VIC calcification. The real-world data analysis revealed that SGLT2i-treated group had a lower incidence of hospitalized patients for non-rheumatic aortic valve disease compared to SU-treated group. Conclusions Our data identify SIRT1 as a key regulator of fibro-calcific processes in AS and suggest that SGLT2i may slow the aortic valve degeneration through SIRT1 modulation. These findings highlight SGLT2i as a promising therapeutic option for AS prevention and care. Clinical Perspectives What is new? Sirtuin 1 (SIRT1) downregulation is linked to the progression of aortic stenosis (AS) pathological processes and plays a crucial role in mitigating oxidative stress, fibrosis, and calcification. Sodium-glucose co-transporter 2 inhibitor (SGLT2i) treatment of valve endothelial cells results in the secretion of protective factors that reduce valve interstitial cell calcification, highlighting the valuable role of endothelial health in preventing valve degeneration. Real-world data indicate that the use of SGLT2i is associated with a lower incidence of hospitalization rate for aortic valve disease as compared to sulfonylureas, suggesting a protective effect against AS in diabetic patients. What are the clinical implications? This study highlights the potential of restoring SIRT1 activity as a therapeutic strategy to mitigate pro-calcific and pro-fibrotic processes in AS. SGLT2i may offer a breakthrough therapeutic option for AS, a condition currently lacking effective pharmacological treatments, providing new hope for slowing disease progression and improving clinical outcomes.

1 Characterization of essential genes across the genome is fundamental to understanding cellular functions at a molecular level. While significant progress has been made in characterizing essential genes in human and mouse models, relatively little is known about essential genes in the porcine genome. Pigs are an important production species and are now emerging as valuable models for studying human diseases due to their physiological similarities to humans. To map essential genes across the porcine genome, we have developed a novel porcine genome-wide CRISPR knockout screening library (pGeCKO) and applied it to two porcine cell lines, PK15 and IPEC-J2. We identified 2,245 essential genes in PK15 cells and 919 essential genes in IPEC-J2 cells, with 683 of these shared between both cell lines. Functional analyses revealed that most essential genes are involved in core cellular processes such as cell cycle regulation, DNA replication, transcription, and translation. Comparative analysis with human essential genes from the DepMap project revealed that over half of the genes are shared with humans and the rest are porcine-specific. These porcine-specific essential genes included genes in core functional pathways related to protein and RNA processing as well as many related to N-glycan biosynthesis, signal transduction, and several long-noncoding RNAs. This work provides a new resource for leveraging porcine models in disease research, enhancing our understanding of porcine genetics and its implications for human health.

PML nuclear bodies (PML-NBs) are dynamic subnuclear structures important for chromatin dynamics and anti-viral defense. In this study we investigate the role of Sp100 isoforms in promoting localization of the H3.3 histone chaperone HIRA to PML-NBs in human keratinocytes. Sp100 knockout (KO) cell lines were generated using CRISPR-Cas9 technology and shown to display normal keratinocyte differentiation and PML-NB formation. However, HIRA and its associated complex members (UBN1 and ASF1a) failed to localize to PML-NBs in the absence of Sp100, even after interferon stimulation. Exogenous expression of the four main isoforms of Sp100 showed that the Sp100A isoform is the primary driver of HIRA localization to PML-NBs, with the SUMO interacting motif (SIM) playing an important role. These findings highlight the functional diversity of the Sp100 isoforms in modulating chromatin dynamics at PML-NBs.

ABSTRACT Serine incorporator 5 (SERINC5) is a host restriction factor that targets certain enveloped viruses, including human immunodeficiency virus type 1 (HIV-1) and murine leukemia virus (MLV). It integrates into the viral envelope from the cell surface, inhibiting viral entry. SERINC5 is transported to the cell surface via polyubiquitination, while a single K130R mutation retains it in the cytoplasm. Both HIV-1 Nef and MLV glycoGag proteins antagonize SERINC5 by reducing its expression in producer cells. Here, we report that MLV glycoGag employs selective autophagy to downregulate SERINC5, demonstrating a more potent mechanism for decreasing its cell surface expression. Although glycoGag is a type II integral membrane protein, it primarily localizes to the cytoplasm and undergoes rapid proteasomal degradation. Employing the K130R mutant, we show that Nef, primarily associated with the plasma membrane, downregulates SERINC5 only after it has trafficked to the cell surface, whereas glycoGag can reduce its expression before reaching the plasma membrane while still in the cytoplasm. Nonetheless, an interaction with SERINC5 stabilizes and recruits glycoGag to the plasma membrane, enabling it to downregulate SERINC5 from the cell surface. Through affinity-purified mass spectrometry analysis combined with CRISPR/Cas9 knockouts, we find that glycoGag’s activity depends on reticulophagy regulator 1 (RETREG1), an ER-phagy receptor. Further knockout experiments of critical autophagy genes demonstrate that glycoGag downregulates cytoplasmic SERINC5 via micro-ER-phagy. These findings provide crucial new insights into the ongoing arms race between retroviruses and SERINC5 during infection. AUTHOR SUMMARY HIV-1 Nef and MLV glycoGag are unrelated viral proteins, yet both counteract the same host restriction factor, SERINC5, to facilitate productive infection. In this study, we report a novel pathway through which glycoGag downregulates SERINC5. We demonstrate that while Nef downregulates SERINC5 only after it has trafficked to the cell surface, glycoGag can directly downregulate SERINC5 in the cytoplasm before it reaches the plasma membrane. Furthermore, we show that this pathway is mediated by the ER-phagy receptor RETREG1, which targets SERINC5 for degradation via micro-ER-phagy. This mechanism provides a more effective means of blocking SERINC5 antiviral activity. These findings reveal that retroviruses have evolved different strategies to antagonize SERINC5, highlighting the critical role of SERINC5 in restricting retroviral infections.

ABSTRACT Producing the gene-knockout mutant is a critical strategy in reverse genetics for gene functional analyses. Plant science has applied various mutagenesis, including chemical mutagen, T-DNA insertion, and genome editing. The intact gene expression is completely disrupted, while the mutant retains the intact sequence region. Lately, effective whole open reading frame (ORF) deletion through the CRISPR/Cas9 system using multiplex guide RNAs was reported in Arabidopsis, targeting a gene expressed in somatic cells. Here we applied the scheme targeting the reproductive genes GENERATIVE CELL SPECIFIC 1 ( GCS1 ), GAMETE EXPRESSED 2 ( GEX2 ), DUF679 DOMAIN MEMBRANE PROTEIN 8 ( DMP8 ), and DMP9 , which are fertilization regulators. Homozygous gene deletion lines were successfully obtained in the T1 generation, with acquisition rates ranging from 8.3% to 30.0%. The rates approximately correlated with the scores predicted by the DeepSpCas9. The analysis of the GCS1 deletion line ( Δgcs1 ) suggested that avoiding the first bolt removal is important for consistent phenotype of the developed inflorescences. Compared to the previously reported mutants, the GEX2 deletion line ( Δgex2 ) showed a difference in seed development phenotype, indicating that the remaining intact gene region in the mutant could unexpectedly influence the function. Simultaneous deletions of DMP8 and DMP9 , which are in distinct chromosomes, were also succeeded in the T1 generation. The obtained results showed that all deletions were inheritable. The scheme challenged here demonstrated the effective production of homozygous mutants for the genes, even if the reproductive lethal or recessive.

ABSTRACT The phenotype of a mutation often differs across genetically distinct individuals. In the most extreme case, a gene can be essential for viability in one genetic background, but dispensable in another. Although genetic context-dependency of mutant phenotypes is frequently observed, the underlying causes often remain elusive. Here, we investigated the genetic changes responsible for differences in gene essentiality across 18 genetically diverse natural yeast strains. First, we identified 39 genes that were essential in the laboratory reference strain but not required for viability in at least one other genetic background, suggesting that the natural strain contained suppressor variants that could bypass the need for the essential gene. We then mapped and validated the causal bypass suppressor variants using bulk segregant analysis and allele replacements. Bypass suppression was generally driven by a single modifier gene that tended to differ between genetic backgrounds. The suppressors often indirectly counteracted the effect of deleting the essential gene, for instance by changing the transcriptome of a cell. Context-dependent essential genes and their bypass suppressors were frequently co-mutated across 1,011 yeast isolates and identified naturally occurring evolutionary trajectories. Overall, our results highlight the relatively high frequency of bypass suppression in natural populations, as well as the underlying variants and mechanisms. A thorough understanding of the causes of genetic background effects is crucial for the interpretation of genotype-to-phenotype relationships, including those associated with human disease.

Understanding how genetic variants drive phenotypic differences is a major challenge in molecular biology. Single nucleotide polymorphisms form the vast majority of genetic variation and play critical roles in complex, polygenic phenotypes, yet their functional impact is poorly understood from traditional gene-level analyses. In-depth knowledge on the impact of single nucleotide polymorphisms has broad applications in health and disease, population genomic or evolution studies. The wealth of genomic data and available functional genetic tools make Drosophila melanogaster an ideal model species for studies at single nucleotide resolution. However, to leverage these resources and potentially combine it with the power of functional genetics to enhance genotype-phenotype research, it is essential to develop techniques to predict functional impact and causality of single nucleotide variants. Here, we present FlyCADD, a functional impact prediction tool for single nucleotide variants in D. melanogaster . FlyCADD, based on the Combined Annotation-Dependent Depletion (CADD) framework, integrates over 650 genomic features - including conservation scores, GC content, and DNA secondary structure - into a single metric reflecting a variant’s predicted impact on evolutionary fitness. FlyCADD provides impact prediction scores for any single nucleotide variant on the D. melanogaster genome. We demonstrate FlyCADD’s utility with some examples of application, including the ranking of phenotype-associated variants to prioritize variants for follow-up studies, evaluation of naturally occurring polymorphisms, and refining of CRISPR-Cas9 experimental design. FlyCADD provides a powerful framework for interpreting impact of any single nucleotide variant in D. melanogaster , thereby improving our understanding of genotype-phenotype connections. Article summary Single nucleotide polymorphisms (SNPs), the most common form of genomic variation, play key roles in micro-evolution and adaptation. In Drosophila melanogaster , many SNPs have been associated to phenotypes through association studies, yet functional validation remains challenging and experimental evidence for functional impact is rare. Here, we present FlyCADD, an impact prediction tool that integrates high-quality D. melanogaster genome annotations into a single score reflecting predicted impact of a SNP. FlyCADD can be applied to distinguish causal from neutral variants, for variant prioritization prior to functional studies, and to enhance interpretation of natural variation, thereby improving our understanding of genotype-phenotype relationships.

A temperate N-15-like phage and an extensively drug-resistant (XDR) Klebsiella pneumoniae strain were studied in this research. The former was found in hospital wastewater, while the latter was retrieved from the sputum of an intensive care unit patient. The bacteria showed strong resistance to several antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). Yersiniabactin, enterobactin, and E. coli common pilus (ECP) genes were also present in the genome; these genes are essential for the acquisition of iron, adhesion, and immune evasion, among other virulence factors. kappa testing categorized the strain as K64 and O2a types. The presence of colicin genes, IncHI1B_1_pNDM-MAR and IncFIB replicons, and other plasmids in this strain demonstrate its ability to spread antibiotic resistance and facilitate horizontal gene transfer. Adding to its genetic variety and adaptability, the genome included CRISPR-Cas systems and eleven prophage regions. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8 percent of ORFs), DNA replication and repair enzymes (9.3 percent of ORFs), and a toxin-antitoxin system (0.4 percent of ORFs) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Lysogeny and horizontal gene transfer are two mechanisms by which phages may influence bacterial evolution. Learning about the phage’s role in bacterial evolution, host-phage relationships, and horizontal gene transfer is a great benefit. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research. Author Summary Antibiotic-resistant bacteria represent a significant global health threat, and comprehending their interactions with bacteriophages is essential for formulating novel antimicrobial tactics and elucidating the molecular development of bacteria. This work examined an extensively drug-resistant (XDR) strain of Klebsiella pneumoniae isolated from an ICU patient and a temperate N-15-like phage identified in hospital effluent. The bacterial strain exhibited resistance to multiple antibiotics owing to an array of resistance genes, plasmids, porin mutations, and virulence characteristics that facilitated its survival and pathogenicity. The genomic investigation of the phage elucidated its structural organization, replication mechanisms, and possible contribution to bacterial development through lysogeny and horizontal gene transfer. Our findings underscore the intricate host-phage interactions that affect antibiotic resistance and pathogenicity in K. pneumoniae, offering significant insights into microbial evolution and the prospective relevance of phages in therapeutic approaches.

Abstract Various cellular stresses release immunogenic molecules and elicit immunosurveillance to detect and eliminate potential threats, thus safeguarding organismal health. Nucleolar stress is characterized by the disruption of nucleolar morphology and function, leading to impaired ribosome biogenesis and activation of stress response pathways. However, the regulatory mechanisms linking nucleolar stress to tumour-intrinsic immunogenicity and its therapeutic implications remain unclear. Utilizing CRISPR screens to identify cancer-specific immunogenic regulators, we identified nucleolar OTUD4 (an ovarian tumour domain-containing deubiquitinase) as a repressor of immunogenicity by preserving nucleolar homeostasis. OTUD4 depletion induced nucleolar stress, thereby enhancing immunogenicity and retarding tumor growth in preclinical models. Mechanistically, OTUD4 functioned as a phospho-activated K63 deubiquitinase, catalyzing the K63-linked deubiquitination of nucleophosmin 1 (NPM1) to stabilize its oligomerization. Consequently, OTUD4 deletion promoted NPM1 hyperubiquitination and depolymerization, thereby driving the release of NPM1-binding heterochromatin H3K9me3. The heterochromatin remodeling derepressed endogenous retroelements (ERV) that subsequently stimulated cytosolic DNA-sensing pathways to trigger the type I interferon response and upregulate the expression of antigen presentation genes. Concurrently, ERV-encoded retroviral antigens augmented tumour-intrinsic antigenicity. A pharmacological screen revealed that the casein kinase II inhibitor CX-4945 phenocopied OTUD4 ablation by dephosphorylating and inactivating OTUD4 activity. Clinically, OTUD4 amplification or a high OTUD4-nucleolus gene signature inversely correlated with patient survival and immunotherapy resistance. Our findings position nucleolar stress as a central driver of tumour-intrinsic immunogenicity, and propose a clinical rationale for leveraging nucleolar stress inducers to sensitize immunologically cold tumours to immunotherapy.