Although hypermutation due to Mut protein mutations that disrupt DNA mismatch repair has been characterized in some bacteria, its mechanisms and consequences in Klebsiella pneumoniae remain poorly defined. We analyzed 11 longitudinal KPC-3 carbapenemase-producing, ST258 K. pneumoniae isolates collected over ∼4 years from an immunocompromised patient with chronic colonization and recurrent infections. After ∼3.3 years, isolates developed ceftazidime–avibactam (CZA)-resistance with restored carbapenem susceptibility, coinciding with emergence of a V76G substitution in a highly-conserved motif in the core of MutH endonuclease. Compared with earlier isolates, mutH V76G -carrying isolates showed greater within-host genomic diversification (69-179 vs. 2–12 SNP differences) and acquired bla KPC-3L169P , encoding an KPC Ω-loop substitution that mediates CZA resistance and re-establishes carbapenem susceptibility. mutH V76G isolates exhibited stepwise increases in meropenem-vaborbactam (MVB) and cefiderocol minimum inhibitory concentrations, plausibly linked to substitutions in KPC, OmpK36 porin, CirA iron transporter and/or EnvZ kinase. Clinical mutH V76G isolates and CRISPR-engineered mutH V76G mutants were hypermutators based on rifampin mutational frequencies. Using isogenic mutant and parent strains, we confirmed that mutH V76G accelerated evolution of CZA and MVB resistance in vitro and in vivo , promoted transfer and uptake of resistance plasmids, and improved bacterial fitness during mouse infections. Resistance evolution in mice recapitulated clinical trajectories, with bla KPC-3 and ompK36 mutations emerging under CZA and MVB exposure, respectively. Phenotypes of mutH V76G and mutH -null strains were comparable, indicating that the V76G substitution largely abrogates MutH function. Our findings reveal MutH-mediated hypermutation as an adaptive mechanism in K. pneumoniae , enabling rapid antibiotic resistance development and plasmid acquisition without fitness cost. Importance Hypermutator bacteria pose a formidable clinical threat by rapidly evolving antibiotic resistance and adapting within the human host. Klebsiella pneumoniae is a major cause of multidrug-resistant infections, yet the contribution of hypermutation to its evolution remains poorly characterized. Analyzing K. pneumoniae isolates collected over ∼4 years from a chronically infected/colonized patient, we demonstrate that emergence of a mutation in mutH ( mutH V76G ), a DNA mismatch repair gene, results in hypermutation phenotypes and rapid accumulation of gene mutations. Both clinical and lab-engineered mutH V76G mutant strains rapidly acquire resistance or reduced susceptibility to new antibiotics like ceftazidime-avibactam, meropenem-vaborbactam and cefiderocol, due to mutations in carbapenemase ( bla KPC-3 ), porin ( ompK36 ) and other genes. mutH V76G -driven hypermutation also enhances horizontal transfer of resistance plasmids and improves K. pneumoniae fitness during mouse infections. This study is important for understanding K. pneumoniae hypermutation as a potent mediator of antibiotic resistance and other phenotypes relevant to human infections.

ecDNA contributes to cancer genetic heterogeneity through random segregation during mitosis. Emerging evidence links ecDNA to immune evasion, but the mechanism remains elusive. Using genetically engineered mouse models of pancreatic ductal adenocarcinoma (PDAC), we show that Kras and Myc oncogenes are amplified either on ecDNAs or as homogeneously staining regions (HSRs) on chromosomes. ecDNA-driven tumors are more aggressive in immunocompetent mice. Single-cell transcriptomic and histological analyses reveal that ecDNA-driven tumors rapidly establish an immunoevasive tumor microenvironment (TME), marked by increased myofibroblastic cancer-associated fibroblasts (myCAFs) and reduced T cell infiltration. Mechanistically, ecDNA heterogeneity generates a subset of cancer cells with extremely high Kras expression, termed super-expressors, which secrete amphiregulin to promote myCAF expansion and suppress T cell infiltration. Clonally organized super-expressors establish an immunoevasive niche in the TME from patients with PDAC. Our findings demonstrate a causal role of ecDNA in TME remodeling, offering insights into cancer heterogeneity and immune evasion.

ABSTRACT Prostate cancer progression is driven by heterogenous genetic, phenotypic, and microenvironmental programs that remain challenging to model experimentally. Existing systems such as genetically engineered mouse models, xenografts, and patient-derived organoids have each advanced mechanistic insight but are limited by genetic scope, scalability, or lack of immune context. To overcome these constraints we developed ProMPt, a genetically-defined syngeneic mouse modelling platform that captures combinations of the most recurrent clinical prostate cancer genomic alterations to enable scalable in vitro and in vivo interrogation of prostate cancer evolution. Tumours derived from ProMPt organoids recapitulate the histologic and molecular diversity of human disease. Cross - species transcriptomic integration and multivariate single-cell analysis under defined culture permutations revealed conserved phenoscapes, highlighting a central role for MYC in disease progression and therapy resistance. Guided by these insights, preclinical intervention studies demonstrated that combined MAPK inhibition and blockade of protein translation synergistically suppressed tumour growth in castration-resistant models. This combination not only suppressed proliferation but also remodelled the tumour immune landscape, underscoring its dual epithelial and microenvironmental effects. Together, these findings establish ProMPt as a versatile framework for linking genotype, lineage plasticity, and therapeutic vulnerability in prostate cancer.

SUMMARY Microproteins represent a vast and functionally important class of genes that remain largely unexplored in plant genomes. Here, we developed DeepMp, a deep learning framework that integrated multi-omics evidence and built the most comprehensive plant microprotein atlas to date, identifying 18,338 high-confidence candidates in maize. The majority of these appear to have originated de novo from regions previously annotated as noncoding, and they show hallmarks of rapid, lineage-specific evolution and pronounced tissue specificity. These novel microproteins were found integrated into core regulatory networks, particularly in organ development and nutrient storage. Focusing on the maize kernel, population-scale analyses linked microprotein expression to natural variation in amino acid content. We functionally validated three grain-filling-specific candidates originating from noncoding regions by CRISPR-Cas9 knockouts, which confirmed their roles as precise modulators of arginine, aspartate, and methionine levels, without pleiotropic effects on kernel morphology. Our study provides a foundational resource and analytical framework, establishes microproteins as a new and functionally important coding layer in maize, and uncovers a previously untapped source of targets for crop improvement.

The role of the immune system in regulating organismal lifespan remains poorly understood. Here, we show that CD4⁺ T cells release “telomere Rivers” into circulation after acquiring telomeres from antigen-presenting cells (APCs). River formation requires fatty acid oxidation at the T cell–APC synapse, which selectively excludes glyceraldehyde 3-phosphate dehydrogenase (GAPDH) from the telomere vesicles. The resulting Rivers are depleted of glycolytic enzymes but enriched in T cell–derived stemness factors, enabling targeted rejuvenation of senescent tissues across multiple organs. In aged mice, adoptive transfer of young or metabolically reprogrammed CD4⁺ T cells triggered River production in vivo , and Rivers isolated from these animals could be transplanted into other aged mice to propagate the rejuvenation phenotype independently of T cells. River therapy extended median lifespan by ∼17 months, with several mice surviving to nearly five years. This immune-driven telomere transfer pathway is conserved across kingdoms, including plants, defining the first systemic, transplantable programme of youth.

Sex in fungi is governed by the mating-type ( MAT ) locus, which exists as bipolar, pseudobipolar, or tetrapolar systems. The significance and impact of MAT on sexual reproduction, however, remain understudied. Furthermore, the evolution of fungal MAT loci shares features with the evolution of sex chromosomes in plants and animals. Pathogenic Cryptococcus species harbor a bipolar system with a large contiguous MAT locus, whereas closely related species, such as the non-pathogen C. amylolentus possess a tetrapolar system with unlinked P/R and HD loci. The HD locus encodes homeobox domain containing proteins that play an important and evolutionarily conserved role in sexual reproduction. Here, we explored the roles of HD genes in sexual reproduction and determined the implications of a tetrapolar to bipolar MAT transition. With a CRISPR–Cas9 system we developed for C. amylolentus , we generated gene deletion mutants and demonstrated that a single compatible Sxi1-Sxi2 pair is necessary and sufficient for mating. By relocating the HD genes to the P/R locus, we found that the artificially generated bipolar configuration led to defective sexual development, which could be partially restored through additional rounds of sexual reproduction. Transcriptomic profiling further revealed that a Sxi1-Sxi2 heterodimeric complex drives expression of genes required for DNA replication and ergosterol biosynthesis during sexual reproduction. These findings provide the first experimental demonstration of a tetrapolar-to-bipolar transition in a tetrapolar mating species, illuminating MAT locus evolution and homeodomain protein functions in Cryptococcus . Importance Sexual reproduction is critical for fungal survival and adaptation, yet the mechanisms driving transitions between mating systems remain unclear. With Cryptococcus amylolentus , we provide the first experimental validation of a mating system transition from its original tetrapolar to an intermediate tripolar to a derived bipolar in a tetrapolar species. We show that HD heterodimers phenotypically govern dikaryotic filamentation and also transcriptionally modulate DNA replication. These findings establish a mechanistic basis for how MAT locus reorganization drives bipolar evolution from an ancestral tetrapolar state and reinforce that fertility depends on the coordinated control of MAT locus architecture and regulatory functions.

Mechanistic understanding of how gene activity is regulated has focussed on the roles of transcription factors at promoters and enhancers, whereas mechanisms capable of globally fine-tuning gene expression through dispersed binding across large genomic regions have received less attention. Here we provide evidence that the essential stem cell transcription factor SALL4 modulates gene expression according to DNA base composition by reading the frequency of its AT-rich target motifs. Using an acute depletion strategy, we establish that SALL4-repressed genes localise to AT-rich genomic domains with high levels of dispersed SALL4 occupancy. While SALL4 is localised within peaks and distributed broadly across the genome, explainable machine learning revealed that its occupancy across the gene body is a strong predictor of transcriptional output. We observed rapid increases in chromatin accessibility and histone acetylation independent of transcriptional activity, suggesting that SALL4 primarily acts upon chromatin, while transcriptional changes are secondary. Accordingly, preventing SALL4 from recruiting the histone deacetylase and nucleosome remodelling corepressor NuRD mimicked a Sall4 -null phenotype in stem cells and animal models. Our findings reveal that SALL4’s interpretation of DNA sequence optimises the global epigenome and transcriptome, a process integral to maintaining the stem cell gene expression programme.

Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique to determine the functionality of a gene by directly perturbing the DNA of the gene. One of the most intriguing recent problems is quantifying the similarity between CRISPR perturbations, for example, whether they upregulate the same set of downstream genes. In this context, genetic convergence refers to the phenomenon where CRISPR disruptions of different genes lead to a similar downstream outcome. Existing methods are mostly heuristic. We present XConTest, a two-step, cross-validated procedure for assessing the genetic convergence problem. The test statistics calculated from that procedure are approximately standard normal when the two perturbations have an orthogonal influence on the cell expression profile. We apply XConTest to two studies: an investigation of the common impact of a suite of autism genes, and a large-scale study of genes associated with immune response to determine sets of genes with common functionality.

Emergomyce s africanus is a thermally dimorphic fungal pathogen endemic to Southern Africa, which can cause fatal systemic infections in persons with advanced HIV disease. Its mechanisms of pathogenesis are not well understood. Characterisation of virulence traits in this pathogen requires appropriate molecular tools for genetic manipulation. Molecular technologies developed for the transformation of H. capsulatum were adapted for use in E. africanus. Agrobacterium -mediated transformation was used to generate a reporter strain expressing green fluorescent protein (GFP). The E. africanus GFP reporter strain facilitated the study of yeast interaction with macrophages in vitro and allowed the identification of infected phagocyte cell types in the mouse lung by flow cytometry. E. africanus could also maintain episomal plasmids with telomere-like sequences to introduce expression constructs without genome modification. Using this plasmid system, RNA interference constructs were used to knock down the expression of cell wall α(1,3)-glucan by targeting the transcripts of the α-glucan synthase ( AGS1 ). An episomal CRISPR/Cas9 system was evaluated for E. africanus , which effectively disrupted GFP in a reporter strain and enabled the generation of a URA5 uracil auxotroph. These tools and strains will facilitate future studies to elucidate the mechanisms of pathogenesis of E. africanus . Importance Emergomyces africanus is an opportunistic fungal pathogen affecting persons with advanced HIV disease in South Africa. The biology and pathogenesis of E. africanus are not well understood, as the importance of the disease caused by this fungus (emergomycosis) has only been recognised in recent years, and molecular studies have been impaired by the lack of genetic technologies. In this work, we describe tools and methods for the genetic modification of this pathogen, which will accelerate future studies investigating how the fungus causes disease in the human host. These essential tools include (1) the ability to create fluorescent reporter strains, such as the green fluorescent protein E. africanus strain described here, which facilitates tracking the spread of the fungus during infection and enhances microscopy studies, (2) methods for knocking down gene expression in E. africanus , and (3) the permanent disruption of genes through CRISPR/Cas9 gene editing.

Pericentromeric heterochromatin (PCH) is delineated by the enrichment of repressive epigenetic modifications, specifically trimethylated histone H3 at lysine 9 (H3K9me3) and DNA methylation (5-methylcytosine), which establish and maintain a condensed, transcriptionally silenced chromatin state. Depletion of either H3K9me3 or DNA methylation in mouse embryonic stem cells (mESCs) induces a permissive chromatin configuration that permits de novo recruitment and deposition of normally excluded Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2), characterized by H2AK119ub1 and H3K27me3 modifications, respectively, at PCH. Here, we demonstrate that H2AK119ub1 and H3K27me3 are independently recruited to hypomethylated PCH using a doxycycline-inducible mESC model allowing modulation of Dnmt1 expression levels and catalytic activity. We further investigate the roles of proposed mediators of PRC1/2 targeting, including SCML2, BEND3, KDM2b, and TET enzymes, in this context, our findings indicate that neither PRC1 nor PRC2 recruitment at hypomethylated PCH depends on these factors. Additionally, our data suggest that the permissive chromatin environment resulting from DNA hypomethylation is the principal facilitator of Polycomb complex spreading, offering novel insights into the mechanisms governing epigenetic modifier dynamics and interactions during periods of DNA methylation reprogramming.

Osteoglophonic Dysplasia (OGD) is an autosomal dominant skeletal dysplasia characterized by impaired bone growth resulting in short stature, severe craniofacial abnormalities, and in some patients FGF23-mediated hypophosphatemia. It is caused by gain-of-function variants in FGFR1, particularly in or near the transmembrane domain of the receptor. We used CRISPR in mice to knock-in the FGFR1 p.N330I variant, chosen based on its association with FGF23 excess. Skeletal phenotyping of this Fgfr1 +/N330I model demonstrated markedly reduced body weight and naso-anal length, shortened long bones, and craniosynostosis, all hallmarks of the human disease. Mutant mice exhibited profound microarchitectural changes in cortical bone and severe disorganization of the growth plate and articular cartilage, driven by decreased cell proliferation and increased apoptosis in skeletal tissues. In addition to osteochondrodysplasia, we noted dramatic increases in plasma FGF23 and hypophosphatemia, driven by upregulated Fgf23 expression and protein levels in bone, with consequent undermineralization. An in vivo ossicle assay allowed longitudinal evaluation of mineral metabolism. We modulated the signaling pathway by repurposing an inhibitor of the overactive receptor, infigratinib, resulting in partial restoration of naso-anal length in treated mutant mice. This first model of OGD offers insights into the disease pathogenesis and open avenues for targeted therapeutic strategies.

Mendel’s law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin–antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster , optimized YYAP strain K 711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

Microglia are increasingly recognized as key regulators of neural circuit development and putative contributors to the pathophysiology of neuropsychiatric disorders such as schizophrenia (SCZ). However, the functional impact of SCZ-associated genes in microglia remains largely unexplored. Here, we performed an arrayed CRISPR targeting screen of 30 schizophrenia-associated genes predicted to be differentially expressed in human microglia-like cells. Target genes were prioritized based on post-mortem transcriptomic relevance and predicted ontology-based roles in phagocytosis pathways. We quantified phagocytic activity and morphological changes following gene targeting using high-content confocal imaging. Key targets, including CYFIP1, MSR1, TREM2, SYK, ITGB2 , ITGAM and IRF8 , modulated phagocytosis and altered morphological properties consistent with activation states, validating their functional roles in microglia. To elucidate transcriptional impact, we further applied a multiplexed RNA sequencing platform across gene targets. These analyses revealed gene-specific transcriptional signatures, implicating divergent pathways related to phagocytic, activation, cytoskeletal, and lysosomal function. Together, these findings demonstrate the utility of CRISPR-based functional genomics in characterizing microglia function and identifying new target genes and mechanisms that may underlie their contributions to schizophrenia pathophysiology.

Abstract Mutations in the GJB2 gene, which encodes Connexin 26 (Cx26), are responsible for the majority of cases of non-syndromic congenital hearing loss in humans. While murine GJB2 knockout models have provided mechanistic insight, anatomical and physiological differences limit their translational relevance. Pigs represent a valuable large-animal model because their auditory anatomy and maturation closely resemble those of humans. This study compared two genome-editing approaches to disrupt GJB2 in porcine oocytes before fertilization: (1) electroporation with CRISPR/Cas9 ribonucleoprotein and (2) microinjection with cytosine base editor (BE3) and single-guide RNAs (sgRNAs). Electroporation produced high mutation rates (70–90%) across three concentrations of Cas9/sgRNA but yielded mostly heterozygous or mosaic blastocysts, with limited homozygous knockouts (< 4%). BE3 achieved precise cytosine-to-thymine conversions that introduced premature stop codons, reaching up to 47% total editing and 20% homozygous nonsense alleles. However, blastocyst formation declined at higher component concentrations. Overall, BE3 produced more predictable mutations than conventional CRISPR/Cas9, although embryo developmental competence was dose-dependent. Both methods effectively targeted GJB2 and demonstrated feasibility of pre-fertilization genome editing in porcine oocytes. These findings establish the groundwork for generating GJB2 -deficient pigs as translational models of Cx26-related congenital deafness and for future evaluation of gene-therapy strategies in a large-animal system.

ABSTRACT LIN-28 is an evolutionarily conserved RNA-binding protein that plays critical roles in regulating pluripotency and cell fate determination during animal development. In Caenorhabditis elegans , lin-28 is an integral component of the heterochronic (developmental timing) gene regulatory cascade. Loss-of-function mutations in lin-28 result in precocious cell fate determination during larval development. Previous studies showed that the proper progression of stage specific cell fates during larval development depends on the progressive downregulation of LIN-28, which is negatively regulated by the lin-4 microRNA through complementary sequences located in the lin-28 3’ UTR. In this study, we employ CRISPR/Cas9 editing of the endogenous lin-28 locus to demonstrate that the robust developmental downregulation of LIN-28 involves contributions from multiple inputs. These include a convergent action of the let-7 family and lin-4 microRNAs via adjacent complementary sites in the lin-28 3’ UTR, in conjunction with the previously described post-translational inhibition of LIN-28 by the lep-5 long non-coding RNA, which all together account for virtually the entirety of LIN-28 repression. Furthermore, through the systematic testing of a series of truncations of the lin-28 3’ UTR, we identify three positive regulatory regions that enhance LIN-28 expression, thereby counterbalancing the negative effects of the let-7 and lin-4 microRNAs and the lep-5 long non-coding RNA.

Glucocorticoids are a widely used, potent class of anti-inflammatory drugs that modulate the expression of hundreds of genes across the genome. Although the glucocorticoid response is primarily carried out by the glucocorticoid receptor (NR3C1, a.k.a. GR), there are many glucocorticoid receptor co-factors that are also essential to the downstream effects. To identify novel factors necessary for the glucocorticoid gene expression response, we used a genome-wide CRISPR screen in A549 lung adenocarcinoma cells. In that screen, we knocked out every gene in the human genome, and measured the effect of expression of the glucocorticoid-induced leucine zipper (GILZ), a classic glucocorticoid-response gene. We identified two chromatin remodeling proteins, SMARCA2 and BPTF, that are essential for GILZ expression. We then evaluated the genome-wide effects of SMARCA2 and BPTF on glucocorticoid-mediated gene expression. BPTF had a highly specific role in the glucocorticoid response, affecting the expression of only a handful of genes, and having virtually no effect on dexamethasone-induced changes in chromatin accessibility. However, SMARCA2 was necessary for 27% of dexamethasone-induced transcriptional changes (152 genes), and ∼7% of dexamethasone-induced changes in chromatin accessibility (586 regions of the genome). Genomic regions with SMARCA2-dependent changes in chromatin accessibility were characterized by high dexamethasone-induced regulatory activity in a massively parallel reporter assay, and dexamethasone-induced increases in transcription factor binding and chromatin states. Taken together, these data suggest that SMARCA2 is critical for chromatin remodeling at a specific set of genomic regions with high regulatory activity, which in turn drive changes in expression for many glucocorticoid-responsive genes.

Kabuki syndrome (KS) is a rare cause of intellectual disability resulting from heterozygous pathogenic variants in the gene encoding the histone methyltransferase KMT2D. A previously established loss-of-function mouse model of KS exhibits key phenotypic features, and therapeutic trials in this mouse model suggest postnatal malleability of neurological symptoms. However, 15-30% of individuals with KS, carry missense variants. To investigate whether missense variants lead to similar phenotypic presentation in mice, we used CRISPR-Cas9 to introduce the KS patient variant R5230H into C57BL/6NTac. Computational and in vitro testing suggests that the R5230H variant does not impair protein stability or loss of enzyme function of KMT2D. Despite a distinct mechanistic basis, our new mouse model ( Kmt2d +/R5230H ) recapitulates most phenotypes of our prior loss-of-function model, including growth deficiency, craniofacial anomalies, and IgA deficiency but not altered neurological function. Kmt2d +/R5230H mice show perinatal lethality and a high frequency of unilateral kidney agenesis, a novel phenotype in KS mouse models. Kmt2d +/R5230H mice provide a unique opportunity to understand the impact of missense variants on KMT2D function and uncover developmental and perinatal abnormalities in KS. Summary statement A novel Kabuki syndrome missense mouse model with intact KMT2D enzymatic function shares most features with prior KS models, except disruption of adult neurogenesis, and exhibits novel unilateral kidney loss.

The β-lactams are critically important broad-spectrum antibiotics, widely used as first-line treatments; however, their effectiveness is increasingly compromised by β-lactamase enzymes. Among these, OXA-type enzymes have expanded to over 400 variants and are highly prevalent in Enterobacteriaceae . Current phenotypic and molecular detection tests have long turnaround times or require specialized equipment, respectively. In this study, we optimize a rapid molecular assay combining a PCR with modified thermal ramp rate (TRR) along with CRISPR-Cas12a fluorescence detection for the bla OXA-1 gene. Using a commercial DNA Taq polymerase (TRR: 2.2 °C/s, annealing and extension hold time: 1 s), amplification time was reduced from 80 to 30 min, enabling detection within 50 min (PCR: 30 min; CRISPR: 20 min). With a locally produced enzyme (hold: 10 s), amplification time was 44 min. The assay achieved an analytical sensitivity of 8 CFU/reaction using commercial DNA Taq polymerase. The accelerated PCR:CRISPR workflow delivers results in less than one hour without compromising technical sensitivity (attomoles range), not requiring high technical expertise, and can be implemented in laboratories with basic molecular biology equipment. Highlights An optimized thermal gradient can reduce the turnaround time of PCR-based detection tests CRISPR-Cas in addition to the modified PCR can detect a gene target in less than an hour The proposed workflow is suitable for implementation with basic molecular biology equipment

Background: /Objectives: Despite the success of statin and PCSK9 inhibitor therapies, significant residual cardiovascular risk persists, driven by atherogenic triglyceride-rich lipoproteins (TRLs) and the independent, causal risk factor, lipoprotein(a) [Lp(a)]. This review aims to elucidate the pathophysiology of three key genetic drivers of this risk—Apolipoprotein C-III (APOC3), Angiopoietin-like protein 3 (ANGPTL3), and Lp(a)—and to comprehensively analyze the groundbreaking efficacy and safety data from 2025 clinical trials for novel RNA-silencing and gene-editing therapies targeting them. Methods: This narrative review synthesizes foundational genetic validation studies with a focused analysis of late-breaking Phase 1, 2, and 3 clinical trial data presented at major 2025 cardiometabolic conferences (AHA 2025, ACC 2025) and simultaneously published in high-impact journals. Results: Landmark 2025 trials demonstrated profound efficacy. (1) For APOC3, the Phase 3 CORE-TIMI 72a/b trials showed the antisense oligonucleotide (ASO) olezarsen not only reduced severe hypertriglyceridemia (sHTG) (up to -72.2%) but also achieved a pivotal 85% reduction in acute pancreatitis events. (2) For ANGPTL3, the first-in-human Phase 1 trial of CTX310 (CRISPR-Cas9) validated in vivo gene editing as a clinical tool, achieving deep, dose-dependent reductions from a single infusion in ANGPTL3 (-73%), triglycerides (-55%), and LDL-C (-49%). (3) For Lp(a), the Phase 2 ALPACA trial of the siRNA lepodisiran demonstrated >94% Lp(a) reduction with unprecedented durability, sustained at >90% at day 540.15 (4) Concurrently, the 2024-2025 pause of the VERVE-101 base-editing trial due to LNP-related toxicity (thrombocytopenia, ALT elevation) and successful 2025 pivot to the reformulated VERVE-102 20 highlighted delivery, not just payload, as a critical safety hurdle. Conclusions: The year 2025 marks a paradigm shift from chronic oral therapy toward long-acting injectable (ASO/siRNA) or permanent "one-and-done" (CRISPR/base editing) treatments for cardiovascular disease. These genetic therapies show immense promise for targeting previously "undruggable" risk factors. Future success now hinges on demonstrating MACE reduction in large cardiovascular outcome trials (CVOTs) and navigating the critical translational hurdles of delivery vehicle (LNP) safety and the long-term, off-target monitoring of in vivo gene editing.

Background: /Objectives: Sickle cells disease (SCD) and -thalassemia are autosomal recessive disorders of erythroid cells due to gene mutations occurring at the level of the -globin gene. The severe forms of these hemoglobinopathies observed in individuals homozygous for these defective genes need intensive treatments, are associated with a poor quality of life and allogeneic hematopoietic stem cell represents the only curative treatment option that can be offered only to a limited proportion of patients. Methods: This work is a narrative review supported by a systematic literature search and analysis. Results: To bypass this limitation, autologous hematopoietic stem cell transplantation has been developed in these patients in which patients’ HSCs are harvested and genetically modified ex vivo, then transplanted back into patients after conditioning for stem cell transplantation. There are two different approaches for gene therapy of hemoglobinopathies’, one based on gene addition or gene silencing using lentiviruses as vectors and the other based on gene editing strategies using CRISPR-Caspase 9 technology or base editing. Several gene therapy products have been successfully evaluated in these patients achieving transfusion independence and correction of hematological abnormalities durable in the time. Conclusions Several gene therapy products have been approved for the treatment of SCD and -thalassemic patients and offer a potentially curative treatment for these patients.

Background Hepatocellular carcinoma (HCC) has a poor prognosis due to its high recurrence rate, even after curative surgery. Epigenetic regulators play a critical role in cancer progression, and the histone methyltransferase SETD8/KMT5A has been reported to be overexpressed in various malignancies. This study aimed to elucidate the role of SETD8/KMT5A in HCC. Methods We investigated SETD8/KMT5A expression in 345 primary HCC resection specimens through immunohistochemical staining. For functional analyses, we conducted loss-of-function study of SETD8/KMT5A using HCC cell lines, including in vitro assays for proliferation, cell cycle, invasion, and RNA sequencing with gene ontology (GO) analysis. Additionally, we performed xenograft experiments in mice and performed similar experiments using the SETD8/KMT5A inhibitor UNC0379. Results All cases were divided into either the SETD8 high-expression (n=197) or low-expression (n=148) groups. The high-expression group exhibited significantly poorer 5-year overall survival and 2-/5-year disease-free survival compared with the low-expression group (both p<0.001). Multivariate analysis indicated that high SETD8 expression was an independent poor prognosis factor in overall (p=0.0255) and disease-free (p=0.0051) survival. SETD8/KMT5A knockdown suppressed proliferation by inhibition of G1 to S phase transition (p<0.001). GO terms were related to cancer progression, including cell adhesion, MAPK-related signaling and chromatin remodeling. SETD8/KMT5A knockout using CRISPR/Cas9 inhibited tumor growth (p<0.01) in vivo . Conclusions SETD8/KMT5A overexpression was associated with poor prognosis and was an independent prognostic factor in HCC. In vitro and in vivo analysis, the inhibition of SETD8 could repress HCC progression through the regulation of cell activity and cell cycle transition.

ABSTRACT During type III CRISPR-Cas immunity in prokaryotes, RNA-guided recognition of viral (phage) transcripts stimulates the Cas10 complex to convert ATP into cyclic oligoadenylates. These act as signaling molecules that bind to CARF proteins and activate their effector domains. Here, we report the structure and function of the Cap1 effector, composed of a pair of transmembrane helices (TM1/2), a CARF-like (CARFL) domain and a domain of unknown function (DUF4579). Cryo-EM studies on apo- and ligand-bound states of Cap1 in glyco-diosgenin detergent revealed the formation of tetrameric complexes in both states, with one cyclic tetra-adenylate molecule bound in a pocket composed by the four CARFL domains. Binding of cA 4 triggers conformational changes that widen an otherwise narrow pore formed by the four TM1/2 domains. In vivo , Cap1 activation results in membrane depolarization, a growth arrest of the bacterial host and the abrogation of the viral lytic cycle. Our findings reveal the mechanistic basis of membrane depolarizarion mediated by cyclic nucleotide signaling during the type III CRISPR-Cas response.

Infectious spleen and kidney necrosis virus (ISKNV), the type species of the genus Megalocytivirus within the family Iridoviridae, is one of the most devastating pathogens affecting global teleost populations. Our previous study confirmed that ISKNV-pORF71 (p71/VP71) is a viral virulence factor by constructing a recombinant virus with ISKNV orf071 deletion (ISKNV-Δ71). In the present study, we further found that compared with ISKNV-WT, the ISKNV-Δ71 mutant is more capable of maintaining mitochondrial membrane potential, alleviating mitochondrial membrane permeabilization, preserving mitochondrial membrane integrity, sustaining lower cytochrome c release, and thereby reducing the apoptosis rate of infected cells. Further investigations demonstrated a strong interaction between p71 and the outer mitochondrial membrane (OMM)-localized voltage-dependent anion channel 2 (VDAC2). At the subcellular level, p71 and mandarin fish VDAC2 (mfVDAC2) are originally localized to the nucleus and mitochondria, respectively. However, in cells co-transfected with p71 and mfVDAC2, robust nuclear translocation of mfVDAC2 was verified. Endogenous mfVDAC2 was also confirmed to undergo nuclear translocation upon ISKNV-WT infection. In the zebrafish infection model, zebrafish VDAC2 (zfVDAC2)—but not zfVDAC-1 or zfVDAC-3—was observed to translocate into the nucleus through interaction with p71. Using CRISPR/Cas9 technology, VDAC2-knockout zebrafish were successfully constructed. Infection experiments showed that ISKNV-Δ71 exhibits significantly reduced lethality to both wild-type zebrafish and zfVDAC2-knockout zebrafish. In conclusion, our findings reveal that p71 exerts its function during ISKNV infection by hijacking VDAC2 into the nucleus, which alters mitochondrial membrane permeability and enhances ISKNV-induced apoptosis. The phenotypic characteristics of VDAC2 knockout (vdac ⁻/⁻ ) zebrafish were also thoroughly analyzed and discussed. Author summary VDAC2, a well-characterized cellular protein localized to the outer mitochondrial membrane (OMM), plays critical roles in viral pathogenesis and antiviral immune escape. Previous studies have shown that VDAC2 interacts directly or indirectly with viral proteins or functions as a functional receptor to modulate viral pathogenesis; however, few studies have demonstrated that VDAC2 is hijacked from its native OMM to other organelles. Our study here provides robust evidence that cellular VDAC2 is rerouted from its original OMM to the nucleus through interaction with ISKNV p71, thereby altering viral pathogenesis. This work offers novel insights into the role of VDAC2 in pathogen virulence. As far as we know, this is the first report demonstrating that host VDAC2 is hijacked into the nucleus by a viral protein to subsequently modulate the viral life cycle. Collectively, these findings advance our understanding of the active regulation of host functional proteins by iridoviruses.

ABSTRACT Approximately 75% of breast cancer cases are estrogen receptor (ER)-positive, with endocrine therapies forming the foundation of treatment. However, therapeutic resistance remains a major clinical challenge, necessitating the identification of new molecular targets. Myosin VI (MVI), a motor protein increasingly linked to cancer, directly interacts with the ER and plays a key role in the spatial regulation of RNA Polymerase II. Notably, expression levels of MVI and ER are positively correlated across breast cancer tissues. Here, we present a multidisciplinary investigation combining advanced imaging, genomic profiling, and phenotypic characterisation to elucidate the interplay between MVI and the ER. We demonstrate that MVI nuclear localisation is dynamically regulated by estrogen signalling and ER activity. Conversely, ER nuclear localisation requires active MVI, suggesting a reciprocal regulatory mechanism. Furthermore, MVI influences subnuclear architecture, modulating ER transcriptional activity and downstream gene expression programmes that govern cell proliferation and migration. Importantly, pharmacological inhibition of MVI enhances the effect of hormone therapy, resulting in greater disruption of ER function than monotherapy alone. Moreover, MVI inhibition also suppresses the activity of hormone-resistant ER mutants, highlighting its potential to overcome therapy resistance. Our findings establish MVI as a critical regulator of ER nuclear dynamics and gene expression, supporting its candidacy as a novel therapeutic target in ER-positive breast cancer.

Plasmodium falciparum , the most virulent human malaria parasite, is transmitted by Anopheles mosquitoes whose community composition varies geographically. Population genomic analyses reveal highly differentiated P. falciparum loci with roles in mosquito infection, which may be driven by adaptation to regional vectors. To test this, we generated transgenic parasites in which reference alleles were replaced with geographically alternative variants at candidate transmission-stage genes. Transmissibility was compared across four mosquito species representing distinct geographic ranges ( An. gambiae , An. stephensi , An. minimus , and An. albimanus ). Two of five tested polymorphisms increased oocyst and sporozoite burdens in sympatric parasite–vector combinations. Both substitutions occurred in ookinete micronemal proteins, CTRP and WARP, within von Willebrand factor A domains, suggesting that regional allelic variation modulates Plasmodium –vector compatibility by altering midgut adhesion interactions.