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.

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.

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 up-regulate 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.

Emergomyces 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.

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 K711 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.

The vertebrate brain develops through a precisely orchestrated sequence of events, where neural progenitors generate neuronal diversity. However, the importance of stem cell origin in the acquisition of functional characteristics and the assembly into circuits are largely unknown. Here, by multimodal cell lineage reconstruction we reveal a link between progenitor origin and excitatory and inhibitory activity in the hindbrain. By combining progenitor intersectional fate mapping with newly developed computational tools and CRISPR/Cas9-based loss-of-function experiments, we discovered the differential temporal contribution of distinct progenitor pools -defined by proneural gene expression- to both glutamatergic and GABAergic neurons. Whereas neurog1-progenitors contribute to both lineages in early embryonic stages, later, other progenitor pools either also assume this role or take over. Using calcium imaging in combination with genetic perturbations, we unveiled that spatiotemporally defined stem cell origin determines specific neuronal activity features. Overall, we provide in vivo evidence for a link between cell ontogeny and functionality in the vertebrate hindbrain.

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.

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.

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 blaOXA-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.

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 Rubella virus (RuV) causes rubella and, when acquired during pregnancy, congenital rubella syndrome (CRS). Despite its clinical significance, the cellular entry mechanism of RuV remains poorly characterized owing to limited knowledge of host receptors, hampering pathogenesis studies and therapeutic development. Here, we identify Nectin-4 as a functional RuV entry receptor through proximity biotin labeling-based proteomics coupled with CRISPR/Cas9 validation. Notably, Nectin-4 is shared with measles virus, revealing convergent evolution in viral entry despite the different viral families. Nectin-4 directly interacts with the RuV envelope glycoproteins through its ectodomain, facilitating receptor-mediated endocytosis following initial calcium-dependent viral attachment. In polarized respiratory epithelial cells, Nectin-4 mediates basolateral viral entry and subsequent apical release of progeny virions, enabling efficient respiratory transmission. Using human placental organoid models, we demonstrate that syncytiotrophoblasts serve as primary targets for transplacental RuV infection, with viral entry significantly inhibited by Nectin-4 blockade. These findings establish Nectin-4 as critical for both horizontal respiratory transmission and vertical maternal–fetal transmission of RuV. Our results provide fundamental insights into RuV pathogenesis and identify Nectin-4 as a promising therapeutic target for CRS. Importantly, the discovery of shared receptor utilization between RuV and measles virus opens new avenues for integrated elimination strategies targeting both pathogens.

Drugs targeting nucleoli and generating nucleolar stress (NS) such as RNA Polymerase I inhibitors have shown anticancer properties with some progressing to clinical trials. However, the mechanisms that modulate the sensitivity to NS remain poorly understood, which has limited the design of clinical trials on patients most likely responding to these therapies. To get a panoramic view of the genetic determinants that shape the response to NS in cancer cells, we conducted genome-wide CRISPR screens in cells treated with 2 independent RNA Polymerase I inhibitors: Actinomycin D (ActD) and BMH-21. As expected, mutations known to regulate the response to NS such as P53 or RB1 increased the resistance to both drugs. On the other hand, the toxicity of RNA Pol I inhibitors was increased in the context of mutations that enhance PI3K/mTOR signaling. Surprisingly, we found mutations that sensitized to ActD but increased the resistance to BMH-21, revealing that, while both drugs are used as RNA Pol I inhibitors, the must have additional unknown targets. Together our study provides a global landscape of the mechanisms that modulate the sensitivity to NS-inducing agents and illustrate the need for an in-depth analysis of the mechanism of toxicity of drugs, particularly when these are advancing to clinical use.

Acute myeloid leukemia (AML) is a heterogeneous malignancy with limited curative treatment options. Transposable elements (TEs) are now recognized as key regulators of genome function, with aberrant activation implicated in cancer. However, their tumor-type-specific roles remain poorly characterized. Using single-cell Perturb-seq, we systematically screened for chromatin-associated regulators in primary AML patient cells to uncover dependencies required for leukemia cell viability. Our screen identified IRF2BP2 as an AML-selective dependency, functioning as a repressor of TE expression. Loss of IRF2BP2 induced differentiation, apoptosis, and impaired leukemic cell fitness, phenotypes linked to transcriptional activation of TEs, particularly evolutionarily young human endogenous retrovirus K (HERV-K). Mechanistically, IRF2BP2 cooperates with TRIM28 and DNMT1 to epigenetically silence TE expression. CRISPR-mediated activation of HERV-K/LTR5_Hs recapitulated the phenotypic effects of IRF2BP2 loss, while targeted re-silencing of HERV-K/LTR5_Hs partially rescued the effects, establishing a causal link between TE regulation and AML maintenance. Our findings highlight tumor-suppressive functions of TEs in leukemia and reveal IRF2BP2 as a key regulator of TE silencing in AML. Targeting the epigenetic machinery governing TE repression may represent a promising therapeutic avenue for differentiation-inducing and immunomodulatory strategies in AML.

Membrane trafficking governs the transport of molecules to both intracellular and extracellular locations, thereby maintaining cell homeostasis. During cancer progression, alterations in membrane trafficking are frequently observed. However, the mechanisms underlying the dysregulation of membrane trafficking in cancer progression remain largely unresolved. Recent evidence has demonstrated that epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma (LUAD) employs a membrane trafficking program to coordinate cancer cell invasion and immunosuppression in the tumor microenvironment (TME). To further dissect the pro-tumorigenic membrane trafficking program, here we conducted a CRISPR interference (CRISPRi) in vivo screen for membrane trafficking regulators in a syngeneic mouse model with a complete immune system. This screen identified REEP2, an endoplasmic reticulum (ER) shaping protein, as a novel regulator of the EMT-dependent membrane trafficking program, which is associated with a poor prognosis in LUAD patients and is required for LUAD metastasis in a syngeneic orthotopic LUAD mouse model. Mechanistically, the EMT activator ZEB1 upregulates REEP2 expression through miR-183- and miR-193a-mediated regulation that promotes the transportation of secretory cargoes from the ER exit site (ERES) to the Golgi, thereby augmenting the secretion of pro-tumorigenic factors. The REEP2-driven secretion promotes cancer cell proliferation, migration, and the infiltration of myeloid-derived suppressor cells (MDSCs) in the TME. These findings identify REEP2 as a critical mediator of the EMT-driven pro-metastatic membrane trafficking program, revealing a specific vulnerability in mesenchymal LUAD.

Background The pathogenic G 4 C 2 repeat expansion in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Studies focused on delineating the underlying perturbed mechanisms resulting from this genetic mutation are often confounded by the heterogeneity present in current disease models, such as patient-derived iPSC lines, with estimations of up to 50% of the variation in iPSC cell phenotypes resulting from inter-individual differences. Isogenic models, in which the pathogenic mutation is introduced into a defined genetic background, offer a powerful approach to isolating mutation-specific effects and enable high-resolution comparison across distinct ALS/FTD-associated mutations. Such models are essential for uncovering convergent disease mechanisms and improving reproducibility in ALS/FTD research. Methods A two-step scarless CRISPR/Cas9 genome editing strategy was used to generate isogenic human iPSC lines carrying a de novo knock-in of a disease-length G 4 C 2 repeat expansion in the C9ORF72 locus. The resulting lines underwent thorough quality control and were differentiated into lower motor neurons and assessed for the presence of key ALS/FTD pathologies, including changes to C9ORF72 mRNA and protein expression, RNA foci and dipeptide repeat proteins. Results Two C9ORF72 knock-in iPSC lines were generated with 631 and 600 G 4 C 2 repeats, alongside an isogenic genome editing control line. The C9ORF72 G 4 C 2 repeat expansion knock-in iPSC lines exhibit both loss-of-function and gain-of-function pathological features characteristic of ALS/FTD. Compared to the parental wild-type KOLF2.1J line and isogenic (wild-type) CRISPR control line, these exhibit a significant reduction in C9ORF72 mRNA and protein levels, the presence of RNA foci accumulation, and a marked increase in poly(GA) and poly(GP) dipeptide repeat protein levels in iPSCs and motor neurons. Conclusions This is one of the first reports of a successful knock-in of the pathogenic C9ORF72 G 4 C 2 repeat expansion into a human iPSC line, establishing a genetically defined and physiologically relevant model of ALS/FTD. These isogenic lines recapitulate both key loss- and gain-of-function disease pathologies, providing a crucial complement to existing patient-derived iPSC banks. By eliminating confounding genetic background variability, these cell lines will enable more precise interrogation of C9ORF72 -linked pathomechanisms and offer a robust platform for comparative studies across the ALS and FTD spectrum, mechanistic investigations, and future therapeutic targeting with enhanced translational relevance.

Polypogon australis (Brong.), a native Chilean grass (Poaceae), is a facultative metallophyte capable of colonizing copper mine tailing dams and adapting to saline and acidic substrates. These traits make it a promising candidate for phytoremediation of metal-contaminated soils. However, the lack of in vitro propagation, callus induction, and somatic embryogenesis protocols limits its use in large-scale applications and genetic improvement. This work aims to establish a reproducible in vitro regeneration system for P. australis . Mesocotyl explants were cultured on Murashige and Skoog (MS) medium supplemented with 2.5 mg L −1 Dicamba. Callus induction was achieved in 38.9% of explants, and 45.5% of embryogenic calli regenerated into plantlets producing leaves and radicles without requiring exogenous organogenesis-inducing hormones. The regenerated plants continued to develop further on MS + sucrose medium, confirming the totipotent capacity of mesocotyl-derived calli. The developed protocol provides a foundation for large-scale propagation and genetic transformation of P. australis . By overcoming propagation bottlenecks, this methodology strengthens the potential of this native metallophyte as a model for phytoremediation and future CRISPR-based biotechnological approaches to enhance copper tolerance and accumulation.

Hepatoblastoma (HB), the most common pediatric liver malignancy, is associated with high cure rates although patients with advanced or recurrent disease have less favorable outcomes. Because patients are invariably <4 years of age, chemotherapies can cause significant long-term morbidities. Immortalized HB cell lines could be of great utility for drug screening, for the identification of novel therapeutic susceptibilities, and for studies requiring highly regulated and/or rapidly changing in vitro environments. However, HB research is hampered by a paucity of established cell lines that could be used for such purposes, with only two human cell lines being readily available and neither of which is representative of the most common HB molecular subtypes. Recently, immortalized cell lines have been derived from murine HBs that are driven by several of the most common oncogenes associated with human tumors. These comprise five distinct groups associated with the deregulation of each of the possible combinations of oncogenic forms of the bcatenin, YAP and NRF2 transcription factors or the over-expression of MYC. All five groups share many of the attributes and molecular signatures of actual human HBs. In addition, they have been used for purposes as diverse as identifying novel molecular targets through the use of CRISPR-based screens and the demonstration that some HB cells can trans-differentiate into endothelial cells that support more robust tumor growth. The experience gained from these models and advances in the propagation of human hepatocytes in mice suggests that it will soon be possible to generate bespoke human HBs and immortalized cell lines.