CRISPR-based nucleic acid diagnostics are a promising class of point-of-care tools that could dramatically improve healthcare outcomes for millions worldwide. However, these diagnostics require nucleic acid pre-amplification, an additional step that complicates deployment to low resource settings. Here, we developed CATNAP ( Ca s t rans - n uclease detection of a mplified p roducts), a method that integrates isothermal linear DNA amplification with Cas12a detection in a single reaction. CATNAP uses a nicking enzyme and DNA polymerase to continuously generate single-stranded DNA, activating Cas12a’s trans -cleavage activity without damaging the template. We optimized enzyme combinations, buffer conditions, and target selection to achieve high catalytic efficiency. CATNAP successfully distinguished between high- and low-risk HPV strains and detects HPV-16 in a cervical cancer crude cell lysate at room temperature with minimal equipment, offering advantages over PCR-based approaches. We conclude that CATNAP bridges the sensitivity gap in CRISPR diagnostics while maintaining simplicity, making accurate disease detection more accessible in resource-limited settings.

Triple-negative breast cancer (TNBC) is a highly aggressive subtype, accounting for 10–15% of breast cancer cases in the United States. Liver metastases, common in advanced TNBC, are linked to especially poor outcomes, with a 5-year survival rate of just 11%. Although immune checkpoint inhibitors (ICIs) targeting PD-1 or PD-L1 show promise, durable responses in TNBC remain uncommon. This is largely due to a profoundly immunosuppressive tumor microenvironment (TME), driven by tumor-associated myeloid cells. Tumor-associated macrophages (TAMs) and neutrophils (TANs) polarize into immunosuppressive M2 and N2 phenotypes, respectively, suppressing T cell activity through cytokines, ROS, and checkpoint ligands such as VISTA. Myeloid-derived suppressor cells (MDSCs) further inhibit immunity by depleting nutrients and inducing regulatory T cells. As a result, despite its immunogenic features, TNBC remains resistant to immunotherapy due to persistent myeloid-mediated suppression. Here, we developed ionizable lipid nanoparticles (iLNPs) engineered to deliver the CRISPR-Cas12a ribonuclease complex targeting Rictor, a critical component of mTORC2, for in vivo reprograming of myeloid cells. The intravenous (IV) injection of CRISPR Rictor-targeting iLNP (CR-Ric-LNP) showed efficient uptake by circulating myeloid cells and accumulation into the breast cancer liver metastases. Notably, Rictor gene editing triggered pro-inflammatory activation of myeloid cells in the TME, enhancing antitumor responses. Single-cell RNA sequencing revealed that Rictor silencing treated samples showed induced rapid remodeling of the TME, with a significant reduction in immunosuppressive macrophages within 24 hours of treatment. Concurrently, cytotoxic T-cell populations exhibited increased interferon-gamma ( Ifng ) production, driving the emergence of specific myeloid clusters that were responsive to Interferon signaling, particularly in macrophages and neutrophils. A shift from an immunosuppressive to an inflammatory TME was further evidenced by an elevated Cxcl10/Spp1 ratio in myeloid cells. CR-Ric-LNP treatment also enhanced T-cell activation, reducing exhausted T cells and regulatory T cells (Tregs) while expanding natural killer (NK) cells, naïve CD4+, and CD8+ T cells. These changes correlated with a decreased proportion of tumor cells and proliferating cells, ultimately leading to a significant survival benefit in a 4T1 breast cancer liver metastasis model. Our findings demonstrate that myeloid-targeted Rictor silencing reprograms the TME, promoting antitumor immunity and improving therapeutic outcomes.

Summary The Yamanaka factors (OCT4, SOX2, KLF4, and MYC; OSKM) can rejuvenate aging phenotypes in somatic cell types by resetting the epigenetic landscape. Curiously, most solid tumor cells remain largely resistant to reprogramming despite their well-documented plasticity, and the underlying mechanisms are unclear. Here, we combined genomic profiling and in vivo assays to investigate OSKM-mediated reprogramming of pancreatic ductal adenocarcinoma (PDAC). In the initial stages, we found that cancer-specific genes were refractory while mesodermal/ECM programs, normally silenced by PRC2, were aberrantly upregulated. A CRISPR interference screen for OSKM reprogramming coupled with functional analyses revealed that suppression of cancer-associated long noncoding RNAs (lncRNAs) erased malignant epithelial programs, restored tumor suppressor activity, and impaired tumorigenicity in vivo . We further identified that ATXN7L3-AS1 lncRNA sustains the PDAC malignant identity through its association with active epithelial oncogenic programs and poised PRC2-targeted developmental genes, thereby supporting both plasticity and memory. Thus, by exploring why cancer cells are resistant to reprogramming, we identify lncRNAs as gatekeepers of malignant identity, suggesting that targeting lncRNAs could be a generalizable therapeutic strategy in treating solid tumors.

RNA-based/associated biosensors represent a rapidly expanding area of research, providing highly sensitive tools for detecting and monitoring RNA in diverse biological contexts. These sensors offer the ability to track RNA localization, modifications, and interactions in real-time, making them particularly well-suited for developmental biology research. Despite their demonstrated utility in fields such as diagnostics, synthetic biology and environmental science, the application of RNA biosensors in developmental biology has only begun to emerge within the past decade. This gap is notable given the potential of these tools to address key questions about spatiotemporal RNA regulation and cellular signaling during development. This perspective review presents a selection of RNA biosensors, including fluorescent RNA aptamers, CRISPR-Cas-based systems, riboswitches, and catalytic RNA sensors, which have gained attraction in other scientific disciplines. These tools can be used not only to study intrinsic RNA biology, such as RNA expression, splicing, and localization, but also to detect the effects of extrinsic physical and chemical factors, including pH, temperature, redox state, and mechanical stress, on RNA behavior during developmental processes. These examples illustrate how RNA biosensors could be adapted to study developmental mechanisms in model organisms, enabling investigations into RNA dynamics and their role in shaping developmental processes. By revisiting these underutilized tools, this review highlights their relevance for advancing the understanding of molecular mechanisms in developmental biology studies.

Hypoxia within the tumor microenvironment poses a major barrier to the efficacy of NK cell-based immunotherapies for solid tumors. In this study, we investigated the influence of hypoxia on NK cell function and mitochondria. We found that hypoxia reduced NK cell cytotoxicity, mitochondrial content, and membrane potential, while increasing mtROS and inducing broad transcriptional changes in metabolic and stress response pathways. CAR engineering with CD70 and IL-15, while designed to enhance persistence and metabolic fitness, did not prevent hypoxia-induced impairment. Given the mitochondrial disruption, we then explored whether DRP1 ablation could mitigate hypoxia-induced dysfunction. Pharmacological inhibition of DRP1 restored mitochondrial content and cytotoxic function. To confirm the role of DRP1, we generated CRISPR-Cas9-mediated DRP1 KO NK cells, which preserved mitochondrial load and membrane potential under hypoxia. When armed with CD70-CAR-IL-15, DRP1 KO cells retained cytotoxic activity under hypoxic conditions. These findings show that DRP1 inactivation can support NK cell function in hypoxic environments, and that metabolic engineering may enhance CAR NK cell efficacy in solid tumors. Graphical abstract NK cells become dysfunctional in hypoxic conditions, while DRP1 KO NK cells retain their function.

Urinary small extracellular vesicles (sEVs), which can reflect systemic conditions, hold great promise for non-invasive cancer diagnostics, yet the mechanism by which tumor-derived sEVs reach urine remains unclear. Here, we demonstrate that the glomerulus actively transcytoses circulating tumor-derived sEVs into urine. Using CRISPR gRNA-tagged glioma sEVs and bioluminescent/fluorescent GeNL-tagged lung and pancreatic cancer sEVs, we tracked their journey from tumors to urine in multiple mouse models. In vivo and in vitro analyses revealed endocytic uptake and transcytotic release by glomerular cells, accompanied by changes in sEV size and surface composition. GeNL-tagged sEVs consistently showed higher signals in urine than plasma, indicating selective excretion. These findings redefine the glomerulus as a dynamic regulator of EV processing and establish a mechanistic foundation for urinary liquid biopsy.

Summary Calcium, as a cellular second messenger, is essential for plant growth. A tip-focused Ca 2+ gradient in polarized cells is considered to drive cell expansion. The cell wall polysaccharide pectin is a major Ca 2+ binding structure and Ca 2+ homeostasis is influenced by the cell wall architecture. LRR-extensin (LRX) proteins are extracellular regulators of cell wall development that are anchored in the cell wall by their extensin domain. The extensin-less LRX1ΔE14 variant of the root hair-expressed LRX1 of Arabidopsis induces a dominant-negative effect resulting in aberrant root hairs. In an effort to identify the underlying mechanism of the root hair defect caused by LRX1ΔE14 , we isolated a su ppressor of dominant- ne gative effect mutant, sune42 . It codes for the CATION CALCIUM EXCHANGER 4 (CCX4) that localizes to the Golgi apparatus and was shown to have Ca 2+ transport activity. A detailed investigation of the Ca 2+ dynamics revealed that LRX1ΔE14 coincides with a defect in tip-focused cytoplasmic Ca 2+ oscillation, and this effect is alleviated by the sune42 mutation. Additionally, reducing Ca 2+ availability influences the LRX1ΔE14 -induced root hair defect. We conclude that sune42 suppresses the root hair defect in LRX1ΔE14 through modulating cytoplasmic Ca 2+ dynamics, pointing at the importance of the Golgi apparatus for cellular Ca 2+ homeostasis.

Telomeric sequences vary across the tree of life and intimately co-evolve with telomere-binding protein complexes. However, the molecular mechanisms allowing organisms to adapt to new telomeric sequences are difficult to gauge from extant species. Here, we reprogrammed multiple yeast lines to human-like telomeric repeats to unveil their molecular and fitness response to novel telomeres. Initially, the exchange of telomere sequences resulted in genome instability, proteome remodelling and severe fitness decline. However, adaptive evolution experiments selected for repeated mutations that drove adaptation to the humanized telomeres. These consisted of the recurrent amplification of the telomere-binding protein TBF1 , by complex aneuploidies, or in repeated mutations that attenuate the DNA damage response. Overall, our results outline a response that defines the adaptive molecular landscape to novel telomeric sequences.

ABSTRACT The decision of naïve T cells to differentiate into a specific Th cell subset after antigen encounter is a critical pivot point of the immune response and, when out of balance, can lead to autoimmunity, allergy or immunodeficiency. Th subset differentiation is determined by the expression of transcription factors including IRF4. We here describe a point mutation (IRF4 L116R ) in the DNA-binding domain of IRF4 leading to a dysregulation of CD4-T cell subsets and their functions. This point mutation does not alter overall protein expression. In sharp contrast to IRF4-null mice, neither the CD4/CD8 ratio nor T cell activation and memory is altered in naïve mice carrying the point mutation. However, IRF4 L116R T cells are reduced in their capability to differentiate into Th1, Th17 and Treg cells in a dose-dependent manner, contrasting with the findings in IRF4 KO T cells. Particularly striking is the loss of Th1-differentiation in T cells from homozygous I rf4 L116R/L116R mice while T cells completely lacking IRF4 show no reduction in Th1 differentiation. Furthermore, despite maintained ability to generate Th17 cells, expression of the IRF4 L116R variant protects mice against disease development in the Th17 cell-dependent EAE mouse model of neuroinflammation. This contrasts with IRF4 knock-out mice, where expression of one wild-type allele of IRF4 is sufficient for full disease development. Together our results show that the L116R point mutation in IRF4 can selectively alter the differentiation and function of some CD4 T cell subsets and suggest that the L116R mutation is not a classical loss- or gain-of-function variant.

Anaplastic thyroid cancer (ATC) is the most aggressive form of thyroid cancer. Despite recent advances in treating BRAFV600E-driven ATC, therapy resistance remains a significant challenge, often resulting in disease progression and death. Leveraging a focused CRISPR/KO screen in parallel with a CRISPR/activation screen, both tailored on response to BRAFV600E inhibitor treatment, we identified TAZ (encoded by the WWTR1 gene) deficiency as synthetically lethal with BRAF inhibitor in ATC. TAZ is overexpressed in ATC compared to well-differentiated thyroid tumors. We demonstrate that TAZ-deficient ATC cells display heightened sensitivity to BRAF inhibitors both in vitro and in vivo . Using gene essentiality score across a large panel of cancer cell lines, we found that BRAFV600E-driven cancers are highly sensitive to TAZ loss, unlike their counterparts with wild-type BRAF and non-BRAFV600E. Mechanistically, we demonstrate that dabrafenib triggers the Unfolded Protein Response (UPR) under ER stress and suppresses protein synthesis. TAZ loss represses the UPR, reverses the inhibition of protein synthesis, and triggers increased cell death by ferroptosis in dabrafenib-treated ATC. Collectively, our findings unveil TAZ as a new target to overcome resistance to BRAF inhibitors in undifferentiated thyroid cancer.

Convergent evolution, the repeated evolution of similar phenotypes in response to the same selective pressures across multiple lineages, is widespread in nature. The extent to which the same genetic mechanisms contribute to convergent evolution could reveal whether the pathway towards these optimal endpoints is flexible or constrained to follow a particular route. Although mimicry of aposematic colour patterns is well known in Lepidoptera, our knowledge of the genetic basis of these convergent patterns is mostly restricted to a few closely-related species. Here we study the genetic basis of mimicry across seven species of Ithomiini and Heliconius butterflies and a day-flying Chetone moth, representing lineages that diverged between ∼1-120 Mya, each presenting similar colour pattern switches. In all the butterfly species, the genetic variants most strongly associated with convergent colour pattern switches are similarly located in non-coding regions near the genes ivory and optix . Colour pattern variation in the moth is associated with a ∼1 Mb inversion around ivory paralleling the supergene architecture of the co-mimic Heliconius numata . In contrast to previous studies in Heliconius , there is limited evidence of alleles shared by means of hybridization in convergence among closely-related ithomiine species. Repeated parallel evolution of regulatory switches via reuse of the same two genes suggests that convergent colour pattern evolution is highly constrained, even across large evolutionary timescales.

Abstract We performed a comprehensive meta-analysis of four major medical innovations (2015–2025) CRISPR gene editing, mRNA vaccines, AI diagnostics, and telemedicine focusing on clinical efficacy, health outcomes, and adoption. For CRISPR therapies in hemoglobinopathies, pooled data from six trials (115 patients) show robust clinical benefits: significant fetal hemoglobin induction, transfusion independence in β-thalassemia, and reduced sickle crises【1,2】. mRNA COVID-19 vaccines exhibited extremely high efficacy; pooled vaccine effectiveness was ~96% (95% CI 93–98%) after two doses【3】, far exceeding traditional platforms. AI diagnostic tools demonstrated moderate accuracy: a meta-analysis of 83 studies found mean diagnostic accuracy ~52% statistically comparable to physicians overall (no significant difference) but lower than expert clinicians【4】. Telemedicine interventions produced modest but positive effects: in a meta-review of 33 RCTs, telemedicine outcomes were at least as good as usual care (Cohen’s d≈0.21) across diverse conditions【5】. Notably, telehealth adoption surged during COVID-19 (e.g. a 683% increase in tele-visits at one center【6】). Comparative analysis indicates mRNA vaccines delivered the largest population-level impact (via prevention of disease), while CRISPR offers potentially curative benefits in niche populations. AI and telemedicine have improved diagnostic and care delivery processes with varying effect sizes. Our findings underscore each innovation’s significant but distinct contribution to global health.

Abstract Leishmania is a protozoan parasite causing leishmaniasis, a disease affecting millions globally. It is transmitted through bites from infected sand-flies, primarily of the Phlebotomus spp. or Lutzomyia spp. The parasite has two main life stages: the promastigote, found in the insect vector, and the amastigote, residing in the macrophages of the host. The mechanisms behind stage differentiation are not well understood. This study shows that redox metabolism modulations are crucial for the life cycle of Leishmania infantum, influencing stage transitions. Inhibiting redox metabolism caused significant morphological changes, from flagellated promastigotes to amastigote-like forms. These changes were evidenced by transcriptomic and metabolomic analyses. RNA sequencing indicated that redox inhibition affected several genes, including one for an iron transporter, LINF_310039600. Using CRISPR-Cas9, knockout mutants of this gene were created, revealing upregulation of amastin, a marker of the amastigote form, underscoring the role of redox metabolism in stage differentiation.

Abstract Pre-harvest sprouting (PHS), where seeds germinate on panicles before harvest under humid conditions, is a serious global issue in cereal crop production, including rice. OsERF94 was previously identified as a candidate gene associated with PHS through a genome-wide association study. In this study, we investigated the role of OsERF94 in PHS using CRISPR/Cas9 gene editing. The CRISPR/Cas9-mediated mutagenesis of OsERF94 induced frameshift mutations, resulting in a loss-of-function of OsERF94 in the 1-I-ET and 2-D-ET lines. The 1-I-ET and 2-D-ET lines exhibited significantly higher germination rates under PHS conditions compared to the wild type, indicating increased susceptibility to PHS. Whole-genome re-sequencing confirmed that few or no mutations could be detected at off-target candidate sites in both edited lines, ensuring the precision of the CRISPR/Cas9 gene editing. A transcriptome analysis revealed that OsERF94 modulates the expression of key GA biosynthetic and catabolic genes, including OsLOL1 , OsKO3 , OsGA3ox2 , and OsGA2ox5 , during both seed development and the early germination stages of PHS. The up-regulation of GA biosynthetic genes and the down-regulation of GA deactivation genes in both gene-edited lines likely led to elevated endogenous GA levels at 0 and 1 days after PHS, promoting germination under PHS conditions. These findings suggest that OsERF94 acts as a negative regulator of germination by modulating both GA biosynthesis and deactivation. Our findings contribute to expanding our knowledge of the molecular mechanisms of OsERF94 in PHS and highlight OsERF94 as a promising target for the genetic improvement of PHS resistance in rice-breeding programs.

Poison exons (PE) are highly conserved exons whose inclusion creates premature termination codons (PTCs) and triggers nonsense-mediated decay (NMD) of the mature transcript. Despite their important role in post-transcriptional regulation, PEs remain poorly annotated due to the lack of systematic transcriptome-wide approaches. Here, we comprehensively investigate the function of PEs in the human brain under physiological and pathological conditions. A comparative analysis of 957 eukaryotic transcriptomes revealed that humans exhibit the highest enrichment of NMD-targeted isoforms. By annotating all splicing events that generate PTCs, we found 12,014 PEs in the human genome. Using GTEx and BrainSpan RNA-seq dataset, we compared PE splicing across tissues and developmental stages and identified 117 PEs uniquely found in the human brain, 1,214 PEs with brain-specific differential splicing, and 1,610 PEs differentially spliced during brain development. By integrating ClinVar variant annotations with SpliceAI predictions, we identified 1,877 pathogenic variants associated with neurological disorders that are predicted to affect the splicing of 891 PEs, and we functionally validated the impact of a subset of them using CRISPR prime-editing in human cells. Our findings highlight PEs as pivotal regulators of gene expression in the human brain and support the therapeutic targeting of PE splicing in neurological diseases. Graphical abstract

The two main cell types in the striatum, dopamine receptor 1 and adenosine receptor 2a spiny projection neurons (D1-SPNs and A2A-SPNs), have distinct roles in regulating motor- and reward-related behaviors. Cre-selective CRISPR-dCas9 systems allow for cell-type specific, epigenomic-based manipulation of gene expression with gene-specific single guide RNAs (sgRNAs) and have potential to elucidate molecular mechanisms underlying striatal subtype mediated behaviors. Conditional transgenic Rosa26:LSL-dCas9-p300 mice were recently generated to allow for robust expression of dCas9-p300 expression with Cre-driven cell-type specificity. This system utilizes p300, a histone acetyltransferase which regulates gene expression by unwinding chromatin and making that region of the genome more accessible for transcription. Rosa26-LSL-dCas9-p300 mice were paired with Drd1-Cre and Ador2a-Cre mice to generate Drd1-Cre:dCas9-p300 and Ador2a-Cre:dCas9-p300 mouse lines and underwent behavioral phenotyping when sgRNAs were not present. Both Drd1-Cre:dCas9-p300 and Ador2a-Cre:dCas9-p300 have cell-type specific expression of spCas9 mRNA. Baseline behavioral assessments revealed that, under a sgRNA absent nontargeted state, Drd1-Cre:dCas9-p300 mice display repetitive spinning behavior, hyperlocomotion and enhanced acquisition of reward learning in comparison to all genotypic littermates. In contrast, Ador2a-Cre:dCas9-p300 do not exhibit any changes in behavior in comparison to their littermates. Electrophysiological recordings of dorsal striatum D1-SPNs revealed that Drd1-Cre:dCas9-p300 mice have increased input resistance and increased spontaneous excitatory postsynaptic current amplitude, together suggesting greater excitatory drive of D1-SPNs. Overall, these data demonstrate the necessity to validate CRISPR-dCas9 lines for research investigations. Additionally, the Drd1-Cre:dCas9-p300 line has the potential to be used to study underlying mechanisms of stereotypy and reward-learning. Significance Statement Using CRISPR-based tools to identify cell-type specific epigenomic and transcriptional mechanisms in disease and behavior has high utility for the neuroscience field. Previous limitations related to implementation of CRISPR-editing systems in mice were thought to be overcome by the generation of transgenic mouse lines, including a novel Cre-dependent dCas9-p300 mouse line. Our data shows however that Drd1-Cre:dCas9-p300 mice, generated from breeding Drd1-Cre mice with the dCas9-p300 mice, have cellular and behavioral disruptions under a nontargeted sgRNA absent state. Overall, these data suggest caution in employing CRISPR-dCas9 systems, particularly transgenic mouse lines, for research investigations.

CRISPR-Cas genome editing toolkits have expanded the scope of genetic studies in various emerging model organisms. However, their applications are limited mainly to knockout experiments due to technical difficulties in establishing knock-in strains, which enables in vivo molecular tagging-based experiments. Here, we investigated knock-in strategies in the harlequin ladybug Harmonia axyridis , a model insect for evolutionary developmental biology, which shows more than 200 color pattern variations within a species. We tested several knock-in strategies using synthetic DNA templates. We found that ssDNA templates generated founder knock-in strains efficiently (2.5-11%), whereas the 5’ regions of ssDNA templates were frequently scraped when the insert length exceeded ∼40 bases. To overcome this limitation, we designed several 3’ extended DNA templates. Of those, fast-annealed 3’-extended double-stranded DNA templates showed extremely high founder generation efficiency (32-67%) and accuracy (67-100%). This strategy is also applicable to the two-spotted cricket Gryllus bimaculatus , demonstrating that the fast-annealed 3’-extended dsDNA template is a highly potent and versatile DNA template for generating knock-in strains in emerging model insects for developmental genetic studies. Summary statement Fast-annealed 3’-extended dsDNA templates facilitate efficient CRISPR-Cas9-mediated knock-in in emerging model insects.

ABSTRACT The human malaria parasite Plasmodium falciparum ( Pf ) expresses ten thrombospondin type 1 repeat (TSR) domain-bearing proteins at different stages throughout its life cycle. TSRs can be modified by two types of glycosylation: O-fucosylation at conserved serine (S) or threonine (T) residues and C-mannosylation at conserved tryptophan (W) residues. Pf TRAP, which is expressed in mosquito-stage sporozoites, has one TSR domain that is O-fucosylated at Thr 256 and C-mannosylated at Trp 250 . We employed site-directed mutagenesis by CRISPR/Cas9 gene editing to generate two Pf TRAP glyco-null mutant parasites, Pf TRAP_T256A and Pf TRAP_W250F. The fitness of these mutant parasites across the life cycle was compared to the parental NF54 wild type as well as a Pf TRAP knockout line. The glyco-null parasites exhibited major fitness defects comparable to knockout: sporozoites were unable to productively colonize the salivary glands and were highly impaired in gliding motility and the ability to invade cultured human hepatocytes. Protein analysis revealed significantly reduced Pf TRAP abundance in the glyco-null mutants despite normal transcript levels. These findings demonstrate that glycosylation of Pf TRAP’s TSR is critical for its proper expression and function, and underscores the importance of TSR glycosylation in the mosquito stage of the life cycle.

Enterococcus faecalis is a gram-positive bacterium and a common cause of hospital-associated infections. Three major CRISPR loci have been discovered in this species, namely CRISPR1-cas, CRISPR2 and CRISPR3-cas. We developed novel primers which target the CRISPR1-cas loci in E. faecalis and tested these primers on 26 E. faecalis isolates isolated from diverse settings from Segamat, Malaysia. Half of the isolates were found to carry the CRISPR1-cas9 locus, and the CRISPR1 array was successfully amplified in 12 out of 13 isolates that contained the cas9 gene. Characterisation of the CRISPR array shows that CRISPR1-cas shares similar array length and typical repeat sequences with CRISPR2 but differ significantly in terms of spacer identities and terminal repeat (TR) sequences. Most CRISPR spacers encode for chromosomal DNA sequences. Genotype characterisation based on ancestral spacer (AS) and TR sequences indicate that E. faecalis with the same CRISPR1-AS genotype do not always harbour same CRISPR2-AS genotypes, and vice versa. A combined CRISPR1-cas and CRISPR2 typing offers comparable discriminatory power to multilocus sequence typing (MLST), suggesting its potential to be used in short-term strain identification and epidemiological surveillance at a lower sequencing cost. Our study provides a genetic reference for future studies in the Southeast Asia region.

Synthetic biology applied to baculoviruses enables genome optimization through the targeted deletion of nonessential genes, enhancing recombinant protein expression. In this study, the CRISPR/Cas9 system with two tandem sgRNAs was used and validated as an efficient strategy to remove independently large genomic fragments from AcMNPV, all encoding proteins dispensable for budded virus production. The resulting mutant viruses were evaluated for their ability to express eGFP and HRPc in Sf9 cells and in Rachiplusia nu and Spodoptera frugiperda larvae. Deletions of the Ac15–Ac16 and Ac129–Ac131 regions led to significant increases in protein expression in infected cells and in larvae. In contrast, deletion of the Ac136–Ac138 region enhanced expression only in cultured cells but had a negative impact on larvae. Removal of the Ac148–Ac150 fragment caused a marked reduction in expression in both experimental systems. These findings confirm that although some genes are nonessential for systemic infection, their combined deletion can differentially affect recombinant protein expression depending on the host. This study validates not only an effective strategy for developing minimized baculovirus genomes but also the use of dual-guide CRISPR/Cas9 editing as a rapid and precise tool for genome engineering in baculovirus-based expression systems.

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor α ( Esr1 ) was significantly increased by HFD, concomitant with a down-regulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 ( Dnmt1 ) and Dnmt3a, and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge; while mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in HFD-challenged mice. Our study demonstrates that DNA methylation at Esr1 promoter plays an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

ABSTRACT Phenotypic plasticity occurs when a genotype can produce more than one phenotype under different environmental conditions. Genetic accommodation allows plastic phenotypes to be tuned to new environments and eventually to even be lost via canalization/assimilation. The colourful and toxic Heliconiini butterflies have biochemical plasticity – they either sequester their cyanogenic glucosides (CG) from their larval hostplant or biosynthesize them when compounds for sequestration are not available. Here, we traced the evolution of CG biosynthesis in Heliconiini butterflies, a fundamental component of this biochemical plasticity. We first CRISPR-edited the CYP405s , which encode the first enzyme of this pathway in Heliconius erato, and confirmed that CYP405 -knockout caterpillars do not biosynthesize CGs. Then, we identified the CYP405 s and CYP332 s (the second gene in this pathway) in 63 species of the subfamily Heliconiinae, as well as in other lepidopterans. Most lepidopterans have a CYP332 , but CYP405 is mostly found in butterflies and has been duplicated in all Heliconius species. Both genes were independently co-opted into CG biosynthesis in the Heliconiinae butterflies and Zygaena moths, in which they were first functionally characterized. Finally, we performed ancestral reconstruction analyses of biochemical plasticity using data from over 700 Heliconiini butterflies. We demonstrated that although plasticity was ancestral in the whole tribe and allowed these butterflies to increase their hostplant range, it might have been lost in few specialized clades, such as the Sapho clade that just sequester CG from their hostplants. This clade has several CYP405 copies, but they lack structurally important P450 domains, which may explain why biosynthesized CGs are virtually lost in species of the Sapho clade. Our findings represent one of the few examples of plasticity-first evolution in which the genetic mechanisms associated with its accommodation/assimilation are known. This study also emphasizes the importance of co-option in the evolution of complex traits, such as toxicity.

Genome-wide association studies (GWAS) have identified numerous loci linked to late-onset Alzheimer’s disease (LOAD), but the pan-brain regional effects of these loci remain largely uncharacterized. To address this, we systematically analyzed all LOAD-associated regions reported by Bellenguez et al. using the FILER functional genomics catalog across 174 datasets, including enhancers, transcription factors, and quantitative trait loci. We identified 42 candidate causal variant-effector gene pairs and assessed their impact using enhancer-promoter interaction data, variant annotations, and brain cell-type-specific gene expression. Notably, the LOAD risk allele of rs74504435 at the SEC61G locus was computationally predicted to increase EGFR expression in LOAD related cell types: microglia, astrocytes, and neurons. Functional validation using promoter-focused Capture C, ATAC-seq, and CRISPR interference in the HMC3 human microglia cell line confirmed this regulatory relationship. Our findings reveal a microglial enhancer regulating EGFR in LOAD, suggesting EGFR inhibitors as a potential therapeutic avenue for the disease.

Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10 -/-embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1 . In situ hybridization studies showed that Rdh10 -/-embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a defect in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development. Highlights The RA requirement for optic cup formation was examined using Rdh10 knockout embryos. Eye RNA-seq and ChIP-seq (H3K27ac) identified Alx1 as a potential RA target gene. Alx1 exhibits RA-regulated H3K27ac deposition near exon 1 associated with a nearby RARE. Alx1 knockout embryos display a misfolded optic cup with a ventral defect similar to Rdh10 KO.

Cerebral small vessel disease is a leading cause of cognitive decline and stroke in the elderly, with cerebral microbleeds (CMBs) as one of the key imaging biomarkers. Our understanding of its pathophysiology remains limited due to the lack of appropriate animal models. We report a novel mouse CMB model created by disrupting collagen IV, a core component of the vascular basement membrane (BM), specifically within brain microvessels. Targeted deletion of Col4a1 was achieved in adult mice using brain endothelial-specific AAV vectors with CRISPR/Cas9. MRI revealed numerous CMBs with distributions similar to those of human CMBs. CMB burden increased progressively over six months following Col4a1 deletion in a dose-dependent manner, accompanied by cognitive decline and motor incoordination. Histological examination revealed hemosiderin deposits corresponding to MRI-detected CMBs without evidence of macroscopic hemorrhage or white matter lesions, while ultrastructural analysis demonstrated significant BM thinning in Col4a1 -depleted microvessels. Analysis of human MRI and genomic data identified significant associations between CMB susceptibility and genetic variants in TIMP2 , an endogenous inhibitor of the matrix-degrading enzyme MMP2, underscoring the clinical relevance of our model. These findings establish a direct causal relationship between microvessel COL4A1 and CMB, suggesting that dysregulated collagen IV homeostasis in BM underlies CMB development.