ABSTRACT Invasive lobular carcinoma (ILC) is a common subtype of breast cancer that is defined in part by genetic loss of CDH1 caused by mutation or deletion, leading to loss of cell adhesion protein E-cadherin in >90% of ILC. Genetic loss of CDH1 is an early event in ILC oncogenesis, yet the mechanisms by which CDH1/ E-cadherin acts as a tumor suppressor are not well understood. To study how early CDH1 loss drives ILC oncogenesis, we used a series of non-transformed human mammary epithelial cell (HMEC) models to target CDH1 /E-cadherin, inhibiting extracellular E-cadherin signaling using antibodies versus modeling genetic CDH1 loss using siRNA or knockout via CRISPR/Cas9. Through transcriptome analyses across four HMEC models, we found that the mode of E-cadherin loss or suppression is critical for the subsequent phenotype. Antibody-mediated inhibition of cell-cell contacts induced gene signatures of epithelial-mesenchymal transition (EMT), consistent with the role of E-cadherin suppression during the EMT process. Conversely, genetic CDH1 loss – as in ILC oncogenesis – repressed EMT signatures, and instead remodeled gene expression toward a luminal epithelial phenotype. Using single cell transcriptomics and flow cytometry analyses of cell lineage markers, we found that genetic loss of CDH1 reprogrammed cells to a luminal progenitor-like phenotype. By isolating luminal versus basal cells prior to CDH1 knockout, we found that CDH1 loss led to remodeling of lineage identity in both populations, converging on a new lineage homeostasis with a luminal progenitor-like phenotype. Consistent with increased progenitor features, CDH1 loss enhanced proliferative capacity over the finite lifespan of the HMECs, highlighting a feature of early CDH1 loss that may contribute to clonal advantage during tumor initiation. Our findings support that inhibition of E-cadherin results in different transcriptional response compared to CDH1 loss, with the latter driving a transcriptional and phenotypic state characteristic of a luminal progenitor-like population, which offers new insight into early events in ILC oncogenesis.

Intercellular communication is essential for distributed genetic circuits operating across cells in multicellular consortia. While diverse signalling molecules have been employed--ranging from quorum sensing signals, secondary metabolites, and pheromones to peptides, and nucleic acids--phage-packaged DNA offers a highly programmable method for communicating information between cells. Here, we present a library of five M13 phagemid variants with distinct replication origins, including those based on the Standard European Vector Architecture (SEVA) family, designed to tune the growth and secretion dynamics of sender strains. We systematically characterize how intracellular phagemid copy number varies with cellular growth physiology and how this, in turn, affects phage secretion rates. In co-cultures, these dynamics influence resource competition and modulate communication outcomes between sender and receiver cells. Leveraging the intercellular CRISPR interference (i-CRISPRi) system, we quantify phagemid transfer frequencies and identify rapid-transfer variants that enable efficient, low-burden communication. The phagemid toolbox developed here expands the repertoire of available phagemids for DNA-payload delivery applications and for implementing intercellular communication in multicellular circuits.

Pediatric cancers pose significant treatment challenges due to their biological heterogeneity and variable responses to chemotherapy. SLFN11, a DNA/RNA helicase-like protein known to sensitize adult tumors to DNA-damaging agents, remains underexplored in pediatric malignancies. Here, we investigate the role of SLFN11 across pediatric Wilms tumor, osteosarcoma, and medulloblastoma using integrated bioinformatics, epigenetic profiling, and functional assays. In silico analysis of TARGET and ICGC datasets revealed distinct correlations between SLFN11 expression and patient survival, with positive, negative, or neutral predictive value depending on tumor type. Baseline expression and promoter methylation analysis in pediatric cancer cell lines demonstrated epigenetic regulation of SLFN11, similar to adult cancers. Using CRISPR-dCas9-mediated activation, we successfully upregulated SLFN11, which significantly enhanced sensitivity to cisplatin and the PARP inhibitor talazoparib across all tested cell lines. Transcriptomic profiling under cisplatin treatment indicated that SLFN11 modulates DNA damage response and MAPK signaling pathways, potentially contributing to chemotherapy sensitivity. These findings establish SLFN11 as a context-dependent predictive biomarker and a potential therapeutic target to overcome chemoresistance in pediatric solid cancers.

Streptococcus agalactiae (group B Streptococcus ; GBS) is a leading cause of neonatal sepsis and meningitis. Despite advances in molecular microbiology, GBS genome engineering remains laborious due to inefficient mutagenesis protocols. Here, we report a versatile and rapid Cas12a-based toolkit for GBS genetic manipulation. We developed two shuttle plasmids—pGBSedit for genome editing and pGBScrispri for inducible CRISPR interference—derived from an Enterococcus faecium system and optimized for GBS. Using these tools, we achieved targeted gene insertions, markerless deletions, and efficient, template-free mutagenesis via alternative end-joining repair. Furthermore, a catalytically inactive dCas12a variant enabled inducible gene silencing, with strand-specific targeting effects. The system demonstrated broad applicability across multiple GBS strains and minimal off-target activity, as confirmed by whole-genome sequencing. This Cas12a-based platform offers a rapid, flexible, and scalable approach to genetic studies in GBS, facilitating functional genomics and accelerating pathogenesis research.

Gliomas are the most common primary intracranial tumors, comprising 81% of malignant brain tumors, and currently lack effective therapies. Recent advances in molecular biology have shown that cancer cells exploit microtubule-associated proteins (MAPs) under stress to activate various signaling pathways. This study investigates the role of Doublecortin (DCX) in glioma metabolism and its impact on tumor proliferation. In this study, CRISPR-engineered glioma models with DCX overexpression or knockdown were analyzed using integrated genomic, transcriptomic, and metabolomic approaches. Metabolic activity was assessed via RNA sequencing, Seahorse assays, and targeted mass spectrometry. Pharmacological inhibition of key pathways validated functional dependencies. We demonstrate that gliomas enriched with DCX exhibit elevated glycolytic activity while also relying on cellular respiration and oxidative phosphorylation (OXPHOS) for energy to support the abnormal proliferation of glioma cells. Upon integrative analysis of enriched genes and proteins, we observed genetic and metabolome-level signatures associated with differences in central carbon and energy metabolism in CRISPR-modified glioma cells expressing high DCX. Whole-genome transcriptome analysis revealed enriched metabolic entities promoting hydrolysis of glutamine and glutaminolysis in glioma cells and inhibition of selected differentially enriched genes with small molecule inhibitors abrogated metabolic enrichment and resulted in reduced energy levels and protein translation required for aberrant growth. Finally, we establish that DCX stimulates glutaminolysis to regulate homeostasis for energy supplements in glioma cells. Targeting DCX-mediated metabolic pathways may provide a novel therapeutic approach for glioblastoma, highlighting the potential for innovative treatments in this challenging disease.

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea against mobile genetic elements, but the role they play in gene exchange and speciation remains unclear. Here, we investigated how CRISPR-Cas targeting affects mating and gene exchange in the halophilic archaeon Haloferax volcanii . Surprisingly, we found that CRISPR-Cas targeting significantly increased mating efficiency between members of the same species, in contrast to its previously documented role in reducing inter-species mating. This enhanced mating efficiency was dependent on the Cas3 nuclease/helicase and extended beyond the targeted genomic regions. Further analysis revealed that CRISPR-Cas targeting promoted biased recombination in favour of the targeting strain during mating, resulting in an increased proportion of recombinant progeny that are positive for CRISPR-Cas. To test whether an increase in recombination is sufficient to increase mating efficiency, we tested whether strains lacking the MRE11-RAD50 complex, which are known to have elevated recombination activity, also exhibited higher mating success. Indeed, these strains showed higher mating, as did cells that were exposed to DNA damage using methyl methanesulfonate. These findings suggest that CRISPR-Cas systems may contribute to speciation by facilitating within-species gene exchange while limiting between-species genetic transfer, thereby maintaining species boundaries.

Efficient, safe, and cell-selective intracellular delivery remains a bottleneck for scalable and cost-effective manufacturing of cell therapies. Here, we introduce Selective Permeabilization using Impedance Cytometry (SPICy) that couples multifrequency single-cell impedance cytometry with real-time, feedback-controlled, low-voltage single-cell electroporation. Electric field focusing in a 3-D printed biconical micro-aperture confines both sensing and electroporation to a microscale zone, enabling continuous-flow operation and the use of low voltages ( 80 %) and high (>90 %) cell viability. Delivery of a range of different cargo sizes (4–500 kDa), GFP mRNA expression, CRISPR-Cas9 based knock-out and delivery to a variety of different cell lines, primary human T cells and peripheral blood mononuclear cells (PBMCs) was also demonstrated. Using heterogenous or mixed samples, selective delivery to both cell lines, and primary immune cell subpopulations, from PBMCs, was demonstrated. SPICy thus provides a label-free, continuous flow, targeted non-viral platform for precision cell engineering.

Mitochondria contribute to compartmentalized metabolism in eukaryotic cells, supporting key enzymatic reactions for cell function and energy homeostasis. However, this compartmentalization necessitates regulated metabolite transport across mitochondrial membranes. Although many transport proteins have been identified, several mitochondrial amino acid transporters remain largely uncharacterized. Using CRISPR-Cas9–mediated candidate transporter knockouts coupled with assessment of metabolite transport via a mitochondrial swelling assay, we identify SFXN1, previously characterized for its role in mitochondrial serine transport, as a protein that mediates mitochondrial transport of a range of other polar neutral amino acids including proline, glycine, threonine, taurine, hypotaurine, β-alanine, and γ-aminobutyric acid (GABA). Furthermore, the SFXN1 paralogues SFXN2 and SFXN3 partially complement loss of SFXN1 to enable glycine transport, while SFXN2 and SFXN5 partially complement loss of SFXN1 to enable GABA transport. Altogether, these data suggest that sideroflexins facilitate the transport of polar neutral amino acids across the inner mitochondrial membrane.

RNA viruses pose significant threats to global health, causing diseases such as COVID-19, HIV/AIDS, influenza, and dengue. These viruses are characterized by high mutation rates, rapid evolution, and the ability to evade traditional antiviral therapies, making effective treatment and prevention particularly challenging. In recent years, CRISPR/Cas13 has emerged as a promising antiviral tool due to its ability to specifically target and degrade viral RNA. Unlike conventional antiviral strategies, Cas13 functions at the RNA level, providing a broad-spectrum and programmable approach to combating RNA viruses. Its flexibility allows for rapid adaptation of guide RNAs to counteract emerging viral variants, making it particularly suitable for highly diverse viruses such as SARS-CoV-2 and HIV. This review discusses up-to-date applications of CRISPR/Cas13 in targeting a wide range of RNA viruses, including SARS-CoV-2, HIV, Dengue, Influenza and other RNA viruses, with the main focus on its potential in therapeutic context. Preclinical studies have demonstrated Cas13’s efficacy in degrading viral RNA and inhibiting replication, with applications spanning prophylactic interventions to post-infection treatments. However, challenges such as collateral cleavage, inefficient delivery, potential immunogenicity as well as development of a concurrent ethical basis must be addressed before clinical translation. Future research should focus on optimizing crRNA design, improving delivery systems, and conducting rigorous preclinical evaluations to enhance specificity, safety, and therapeutic efficacy. With continued advancements, CRISPR/Cas13 holds great promise as a revolutionary antiviral strategy, offering new solutions to combat some of the world’s most persistent viral threats.

Abstract Wildlife crime—including illegal poaching, breeding, and trafficking—is the second most widespread form of transnational crime globally, generating over USD $20 billion annually. These illicit activities not only drive numerous species toward extinction but also destabilize ecosystems, threaten public health through zoonotic spillovers and disrupt the socio-economic stability of communities that rely on biodiversity. The growing scale and complexity of these crimes demand advanced forensic approaches that can deliver robust, legally admissible evidence. With the advent of the genomic era, molecular technologies have revolutionized wildlife forensics by enabling precise species and sex identification, individual assignment, and population tracking. This review explores the integration of genomic tools—including DNA barcoding, short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), whole genome sequencing (WGS), and environmental DNA (eDNA) approaches—into wildlife crime investigations. Special focus is given to cutting-edge techniques such as CRISPR-based species detection, metagenomics for tracking the illegal wildlife trade, and the deployment of portable sequencers for in-field genotyping. The review also addresses pressing challenges and limitations such as the ethical use of genetic data, concerns about biopiracy, and the complexities of integrating genomic evidence into judicial and conservation frameworks. By analyzing the technological, ethical, and policy dimensions of genomics in wildlife forensics, this paper aims to guide researchers, law enforcement agencies, and policymakers toward a cohesive strategy for combating poaching and illegal wildlife trade in the genomic era.

Summary Neurological diseases (NDs) are a major source of unmet medical need, and translational insights have been hampered by complex underlying pathophysiologies and limitations of experimental models. Noncoding single nucleotide polymorphisms (SNPs) at hundreds of loci have been linked to ND risk by genome-wide association studies (GWAS), but the causal genes and pathways are largely unknown. Despite the multicellular pathology of complex traits like multiple sclerosis (MS), functional studies that aim to characterize the molecular impact of disease-associated SNPs often investigate all SNPs linked to disease in the same cellular context. Here, we combine a computational approach to predict the pathogenic cell type of individual risk loci with functional CRISPR perturbation studies in iPSC-derived microglia cells (iMGLs). ND SNP enrichment in cell type-specific enhancers is similar between primary and iPSC-derived cells, and mechanistically supported by shared enhancer-promoter interactions. We apply a novel Perturb-seq platform to interrogate MS risk SNPs in iMGL, identifying likely cis -acting causal risk genes at 5 of 9 loci, as well as downstream differentially expressed genes (DEGs). Despite being found in trans to MS risk SNPs, downstream DEGs are substantially enriched for MS heritability. Downstream DEGs from all 5 target genes show significant overlap, converging on genes related to cytokinesis, phagocytosis, and mitochondrial metabolism. We then compared downstream DEGs to gene expression patterns observed in MS patient tissue studies and observed marked similarities, demonstrating that genes dysregulated as the result of GWAS loci perturbation mirrored effects observed in microglia found in MS patient lesions. Collectively, these results demonstrate that cell type aware functional studies can be used to translate ND SNP associations into mechanistic insights and reveal novel convergent biological mechanisms underlying complex traits.

SUMMARY The von Hippel-Lindau tumor suppressor (VHL) is a component of a ubiquitin ligase complex that normally controls cellular responses to hypoxia. Endogenous VHL is also utilized by proteolysis-targeting chimera (PROTAC) protein degraders, a promising class of anti-cancer agents. VHL is broadly essential for cell proliferation, yet it is a key tumor suppressor in renal cell carcinoma. To understand the functional consequences of VHL loss, and to identify targeted approaches for the elimination of VHL null cells, we have used genome-wide CRISPR-Cas9 screening in human renal epithelial cells. We find that, upon VHL loss, the HIF1A/ARNT complex is the central inhibitor of cellular fitness, suppressing mitochondrial respiration, and that VHL null cells show HIF1A-dependent molecular vulnerabilities that can be targeted pharmacologically. Combined VHL/HIF1A inactivation in breast and esophageal cancer cells can also provide resistance to ARV-771, a VHL-based bromodomain degrader that has anti-cancer activity. HIF1A stabilization can thus provide opportunities for early intervention in neoplastic VHL clones, and the VHL-HIF1A axis may be relevant for the development of resistance to the emerging class of PROTAC-based cancer therapies.

Abstract Nucleoredoxin (NRX), a member of the thioredoxin (TRX) superfamily, is involved in regulating plant growth and development, as well as abiotic and biotic stress processes, but it is not clear whether NRX participates in regulating the drought resistance of foxtail millet. In this study, the SiNRX1 of foxtail millet was knocked out using CRISPR/Cas9 system, and the drought resistance of sinrx1 mutants was identified at both the germination stage and the seedling stage. Moreover, through transcriptome sequencing and data-independent acquisition (DIA) quantitative proteomics determination of sinrx1 mutants and wild types (WT) at the seedling stage under drought and control conditions, the molecular mechanism of SiNRX1 regulating drought resistance was preliminarily analyzed. The results indicated that after 7 days of simulated drought treatment during the germination period, the germination rate, root length and bud length of the sinrx1 mutant decreased significantly in comparison with the WT. During the seedling stage under drought stress, the survival rate, chlorophyll content, proline content, peroxidase (POD) activity and catalase (CAT) activity of the sinrx1 mutant decreased markedly compared to those of the WT plants. However, the malondialdehyde (MDA) content of the sinrx1 mutant was significantly higher than that of the WT. This indicates that, during the germination and seedling stages, the drought resistance of the sinrx1 mutant decreased significantly compared to that of the WT. The transcriptome findings suggested that the 2253 differentially expressed genes (DEGs) (1179 up-regulated DEGs and 1074 down-regulated DEGs) are drought-responsive genes specifically influenced by SiNRX1 . The proteomic results suggests that the 155 differentially expressed proteins (DEPs) (127 up-regulated DEPs and 28 down-regulated DEPs) are drought-responsive proteins specifically influenced by SiNRX1. Moreover, 2253 DEGs and 155 DEPs were significantly and jointly enriched in the phenylpropanoid biosynthesis pathway. This study offers theoretical guidance for the analysis of the drought resistance mechanism of foxtail millet plants and for drought resistance breeding.

Potato late blight, caused by the oomycete pathogen Phytophthora infestans , is one of the most devastating diseases affecting potato crops in the history. Although conventional detection methods of plant diseases such as PCR and LAMP are highly sensitive and specific, they rely on bulky and expensive laboratory equipment and involve complex operations, making them impracticable for point-of care diagnosis in the field. Here in this study, we report a portable RPA-CRISPR based diagnosis system for plant disease, integrating smartphone for acquisition and analysis of fluorescent images. A polyvinyl alcohol (PVA) microneedle patch was employed for sample extraction on the plant leaves within one minute, the DNA extraction efficiency achieved 56 μg/mg, which is ∼3 times to the traditional CTAB methods (18 μg/mg). The system of RPA-CRISPR-Cas12a isothermal assay was established to specifically target P. infestans with no cross-reactivity observed against closely-related species ( P. sojae , P. capsici ). The system demonstrated a detection limit of 2 pg/μL for P. infestans genomic DNA, offering sensitivity comparable to that of benchtop laboratory equipment. The system demonstrates the early-stage diagnosis capability by achieving a ∼80% and 100% detection rate on the third and fourth day post-inoculation respectively, before visible symptoms observed on the leaves. The smartphone-based “sample-to-result” system decouples the limitations of traditional methods that rely heavily on specialized equipment, offering a promising way for early-stage plant disease detection and control in the field.

Senescence has been shown to contribute to the progression of aging related diseases including degenerative disc disease (DDD). However, the mechanisms regulating senescence in the intervertebral disc (IVD) and other tissues/diseases remain poorly understood. Recently, in a CRISPRa genome-wide screen, our lab identified a previously uncharacterized zinc finger protein, ZNF865 (BLST), that regulates a wide array of genes related to protein processing, cell senescence and DNA damage repair. Here, we demonstrate that ZNF865 expression is correlated with age and disease state in human patient IVD samples and mouse IVD. Utilizing CRISPR-guided gene modulation, we show that ZNF865 is necessary for healthy cell function and is a critical protein in regulating senescence and DNA damage in intervertebral disc cells, with implications for a wide range of tissues and organs. We also demonstrate that downregulation of ZNF865 induces senescence and upregulation mitigates senescence and DNA damage in human nucleus pulposus (NP) cells. Importantly, upregulation of ZNF865 shifts the chromatin landscape and gene expression profile of human degenerative NP cells towards a healthy cell phenotype. Collectively, our findings establish ZNF865 as a novel modulator of genome stability and senescence and as a potential therapeutic target for mediating senescence/DNA damage in senescence related diseases and disorders. Summary Degenerative disc disease (DDD) is a major contributor to chronic low back pain, a leading cause of disability globally 1–3 . Cellular senescence has emerged as a key driver of disc degeneration 4,5 , characterized by cell-cycle arrest and the secretion of pro-inflammatory and matrix-degrading factors collectively termed the senescence-associated secretory phenotype (SASP). While the pathological role of senescent cells in musculoskeletal aging is increasingly recognized 6–8 , the upstream molecular regulators remain poorly understood. Here we identify a previously uncharacterized zinc finger protein, ZNF865, as a novel regulator of senescence and genomic stability in human nucleus pulposus (NP) cells. CRISPRi-mediated downregulation of ZNF865 in healthy NP cells induced senescence, increased expression of p16 and p21, and led to increases in DNA damage. Conversely, upregulation of ZNF865 in degenerative NP cells restored proliferation, suppressed senescence markers, reduced DNA damage, significantly diminished SASP factor secretion and restored transcriptomic and epigenetic profiles to a healthy phenotype. This study represents the first functional characterization of ZNF865 and establishes it as an important regulator for senescence in disc cells. These findings highlight ZNF865 as a promising therapeutic target for mitigating senescence-driven pathologies in DDD and potentially other age-related disorders.

CRISPR-associated transposons (CAST) enable programmable, RNA-guided DNA integration, marking a transformative advancement in genome engineering. A central player in the type V-K CAST system is the AAA+ ATPase TnsC, which assembles into helical filaments on double-stranded DNA (dsDNA) to orchestrate target site recognition and transposition. Despite its essential role, the molecular mechanisms underlying TnsC filament nucleation and elongation remain poorly understood. Here, multiple-microsecond and free energy simulations are combined with deep learning-based Graph Attention Network (GAT) models to elucidate the mechanistic principles of TnsC filament formation and growth. Our findings reveal that ATP binding promotes TnsC nucleation by inducing DNA remodelling and stabilizing key protein-DNA interactions, particularly through conserved residues in the initiator-specific motif (ISM). Furthermore, GNN-based attention analyses identify a directional bias in filament elongation in the 5′→3′ direction and uncover a dynamic compensation mechanism between incoming and bound monomers that facilitate directional growth along dsDNA. By leveraging deep learning–based graph representations, our GAT model provides interpretable mechanistic insights from complex molecular simulations and is readily adaptable to a wide range of biological systems. Altogether, these findings establish a mechanistic framework for TnsC filament dynamics and directional elongation, advancing the rational design of CAST systems with enhanced precision and efficiency.

Human Immunodeficiency Virus-1 (HIV) remains a major global public health challenge, having led to over 42.3 million deaths since its discovery in the early 1980s. Despite progress in prevention and treatment, around 60% of people with HIV (PWH) remain undiagnosed in resource-limited regions, disproportionately affecting vulnerable populations and underserved communities across the world. This illustrates the critical need for accessible, accurate, and equipment-free diagnostic tools to enhance detection and thus provide opportunities to curb its spread. Here, we developed a low-cost, robust, and label-free rolling circle amplification (RCA)-rCRISPR diagnostic platform for detecting HIV viral load with minimal instrumentation. Our strategy, combining the integration of RNA-detecting RCA reaction with plasmid reporter-based ratiometric CRISPR (rCRISPR), enables sensitive detection of unprocessed RNA targets without the need for intensive sample pre-treatment. This label-free RCA-rCRISPR diagnostic platform detected HIV RNA down to single-digit aM sensitivity (~3000 copies/mL) from PWH-derived HIV samples ex vivo . Unlike typical RCA, which requires sample fragmentations to break long RNA target sequences, our design harnesses the triple functions of the phi29 DNA polymerase (namely exonuclease activity, polymerization, and strand displacement), enabling the detection of the entire HIV genome without pre-fragmentation. For point-of-care (POC) applications, we constructed an all-in-one smartphone-based minigel electrophoresis device to facilitate equipment-free HIV viral load testing, making it accessible to resource-limited communities. Additionally, the assay has demonstrated the ability for point mutation detection ( BRAF mutation in canine urothelial carcinoma), showcasing the robustness of our strategy for broad disease diagnostic applications.

ABSTRACT Pneumocystis species are obligate fungal pathogens that cause severe pneumonia, particularly in immunocompromised individuals. The absence of robust genetic manipulation tools has impeded our mechanistic understanding of Pneumocystis biology and the development of novel therapeutic strategies. Herein, we describe a novel method for the stable transformation and CRISPR/Cas9-mediated genetic editing of Pneumocystis murina utilizing extracellular vesicles (EVs) as a delivery vehicle. Building upon our prior investigations demonstrating EV-mediated delivery of exogenous material to Pneumocystis , we engineered mouse lung EVs to deliver plasmid DNA encoding reporter genes and CRISPR/Cas9 components. Our initial findings demonstrated successful in vitro transformation and subsequent expression of mNeonGreen and Dhps ARS in P. murina organisms. Subsequently, we established stable in vivo expression of mNeonGreen in mice infected with transformed P. murina for a duration of up to 5 weeks. Furthermore, we designed and validated a CRISPR/Cas9 system targeting the P. murina Dhps gene, confirming its in vitro cleavage efficiency. Ultimately, we achieved successful in vivo CRISPR/Cas9-mediated homologous recombination, precisely introducing a Dhps ARS mutation into the P. murina genome, which was confirmed by Sanger sequencing across all tested animals. Here, we establish a foundational methodology for genetic manipulation in Pneumocystis , thereby opening avenues for functional genomics, drug target validation, and the generation of genetically modified strains for advanced research and potential therapeutic applications. IMPORTANCE Pneumocystis species are obligate fungal pathogens and major causes of pneumonia in immunocompromised individuals. However, their strict dependence on the mammalian lung environment has precluded the development of genetic manipulation systems, limiting our ability to interrogate gene function, study antifungal resistance mechanisms, or validate therapeutic targets. Here, we report the first successful approach for stable transformation and CRISPR/Cas9-based genome editing of Pneumocystis murina , achieved through in vivo delivery of engineered extracellular vesicles (EVs) containing plasmid DNA and encoding CRISPR/Cas9 components. We demonstrate sustained transgene expression and precise modification of the dhps locus via homology-directed repair. This modular, scalable platform overcomes a long-standing barrier in the field and establishes a foundation for functional genomics in Pneumocystis and other obligate, host-adapted microbes.

Prokaryotic microorganisms coexist with mobile genetic elements (MGEs), which can be both genetic threats and evolutionary catalysts. In Haloferax lucentense , a halophilic archaeon, we have recently identified an unusual genomic arrangement: a complete type I-B CRISPR-Cas system encoded on a mega-plasmid coexists with a partial counterpart within an integrated provirus in the main chromosome. The provirus-encoded system lacks the adaptation genes ( cas1, cas2 , and cas4 ), suggesting its potential reliance on the plasmid-encoded CRISPR-Cas module for the acquisition of new spacers. This arrangement suggests a potential instance of “adaptive outsourcing,” where a provirus might leverage a co-resident MGE for a key function. Through comparative genomics, we show that similar proviral CRISPR-Cas systems are found in distantly related haloarchaea (e.g., Natrinema and Halobacterium ), indicating probable virus-mediated horizontal transfer and suggesting they may function as mobile defense modules. Phylogenetic analysis highlights distinct evolutionary origins of the two systems: the plasmid system clusters with other Haloferax CRISPR-Cas systems, while the proviral system clusters with those from other genera, consistent with horizontal acquisition. Interestingly, spacer analysis reveals that the proviral systems predominantly target viral sequences, while the plasmid system appears to target both plasmids and viral sequences, a distribution mirroring broader trends observed in other plasmid- and chromosome-encoded CRISPR systems. This observed targeting preference suggests a potential for complementarity that could support a model of cooperative immunity, where each system may protect its genetic “owner” from competition and, indirectly, the host.

Abstract Characterizing the protospacer adjacent motif (PAM) requirements of different Cas enzymes is a bottleneck in the discovery of Cas proteins and their engineered variants in mammalian cell contexts. To overcome this challenge and to enable more scalable characterization of PAM preferences, we develop a method named GenomePAM that allows for direct PAM characterization in mammalian cells. GenomePAM leverages genomic repetitive sequences as target sites and does not require protein purification or synthetic oligos. GenomePAM uses a 20-nt protospacer that occurs ~16,942 times in every human diploid cell and is flanked by nearly random sequences. We demonstrate that GenomePAM can accurately characterize the PAM requirement of type II and type V nucleases, including the minimal PAM requirement of the near-PAMless SpRY and extended PAM for CjCas9. Beyond PAM characterization, GenomePAM allows for simultaneous comparison of activities and fidelities among different Cas nucleases on thousands of match and mismatch sites across the genome using a single gRNA and provides insight into the genome-wide chromatin accessibility profiles in different cell types.

Plants have long adapted to the earth’s changing environmental patterns. Yet, 1 with the current rise of abiotic stresses, such as salinity, temperatures, drought, and nutrient 2 depletion occurring at unpredictable rates threaten global agriculture. If this pattern keeps 3 continuing, then long-evolved regulatory mechanisms can become inadequate to keep 4 pace with environmental disturbances. Consequently, to work through these challenges, 5 human-targeted genetic interventions are requisite. In this review, the recent advancements 6 in plant resilience research, from evolutionary mechanisms (polyploidy, epigenetics, gene 7 duplication, etc.) to modern synthetic technologies (CRISPR-Cas, transgene technology, 8 nanotechnology, and artificial intelligence (AI)), are discussed to redefine the boundaries of 9 plant stress tolerance. By integrating these two domain principles, we can understand how 10 the evolutionary mechanisms can help us in designing precision tools to retain or integrate 11 the lost valuable genetic characteristics. Despite these advancements, major hurdles such 12 as limited field trials, specific isoform functional data, and plants’ ability to adopt these 13 resilient traits still remain. With human interventions and technological strategies, we can 14 improve the plant’s resilience. Here we are not replacing natural evolutionary adaptation, 15 but rather we are building a path for better plant adaptation in these environmental crisis 16 situations and laying the road to sustainable food systems.17

Diabetes and its retinal complication, diabetic retinopathy (DR), are a rapidly increasing health, societal and economic burden. Diabetic retinopathy is a complex disease with a chronic inflammatory component mediated by retinal microglial cells. Recent studies have demonstrated the importance of the Hippo pathway kinases, Ndr1/Stk38 and Ndr2/Stk38l , in the regulation of macrophages, immune cells that share similarities with microglial cells. However, the role of NDR2 kinases in microglial inflammatory response and in the pathophysiology of diabetic retinopathy has not yet been uncovered. This study investigates the role of NDR2 kinase in microglial cells, particularly in response to high glucose (HG) conditions. Using CRISPR-Cas9, we downregulated Ndr2 kinase in BV-2 microglial cells and analyzed the impact on cellular metabolism, phagocytosis and migratory capabilities. We demonstrate that microglial cells expressed NDR2 kinase protein, especially in HG conditions, suggesting its importance in regulating microglial functions during hyperglycemia. Ndr2 downregulated cells present a decreased basal respiration, indicating an impaired mitochondrial function. They also showed decreased metabolic flexibility to stress conditions, such as adaptation to HG conditions. Functionally, Ndr2 downregulation led to decreased phagocytic capacity and migration of microglial cells, both cytoskeleton-based functions. Furthermore, Ndr2 downregulation resulted in altered cytokine and chemokine secretion profiles. Notably, increased levels of pro-inflammatory cytokines such as IL-6, TNF, IL-17 and IL-12p70 were observed in Ndr2 downregulated cells, even under normal glucose conditions. In conclusion, our findings indicate that NDR2 kinase is crucial for microglial metabolic adaptation to stress, such as high glucose exposure and for influencing microglial inflammatory responses. Therefore, NDR2 kinase plays a vital role in maintaining microglial functional plasticity in response to glucose variations, suggesting potential implications for neuroinflammatory processes in conditions like diabetic retinopathy. Graphical abstract Research in Context What is already known about this subject? The pathogenesis of diabetic retinopathy (DR) involves chronic inflammation mediated by retinal microglial cells, which contribute to vascular damage and neurodegeneration. Microglial dysfunction under high glucose (HG) conditions exacerbates cytokine release and oxidative stress, driving DR progression. NDR kinases regulate inflammatory pathways in macrophages, but their role in microglia during DR was previously unexplored. What is the key question? How do NDR2 kinase regulate microglial inflammatory responses and functional adaptability in diabetic retinopathy? What are the new findings? NDR2 expression is upregulated in microglia exposed to HG. Ndr2 downregulation in microglia impairs metabolic flexibility, phagocytosis, and migration. Ndr2 downregulation disrupts cytoskeleton-dependent microglial functions, limiting their ability to adapt to metabolic stress. Ndr2 downregulation in microglia increases pro-inflammatory cytokines (IL-17, TNF) and reduces anti-inflammatory factors (sTNFRI, VEGF), exacerbating inflammation. How might this impact clinical practice? Targeting Ndr2 signaling could emerge as a therapeutic strategy to modulate microglial-driven inflammation, potentially slowing DR progression and complementing existing glycemic control approaches.

B cell malignancies, including chronic lymphocytic leukemia (CLL) and diffuse large B cell lymphoma (DLBCL), rely on dysregulated B cell receptor (BCR) signaling for survival and proliferation. Prohibitin 1 and 2 (PHB1, PHB2) are multifunctional proteins involved in mitochondrial function, IgM-type BCR signaling and other key oncogenic pathways, making them potential therapeutic targets in lymphomas. Here, we assessed the effects of five PHB-targeting small molecules - FL3, Mel6, Mel56, IN44, and Fluorizoline - on lymphoma cell lines as proof-of-concept study. PHB transcript and protein quantities were differentially affected and distinct patterns of antiproliferative effects and viability were observed. Across cell models, FL3, Mel56, and Mel6 displayed strongest effects. FL3 and Mel56 exerted strong cytotoxic effects, while Mel6 primarily slowed proliferation. IN44 showed modest but selective cytotoxic effects in an ABC-DLBCL model, while Fluorizoline selectively stopped proliferation of a Burkitt lymphoma model. Non-malignant stromal cells remained largely unaffected by Mel56, highlighting a potential therapeutic window of this inhibitor. Replacing the native IgM constant region by IgG in the MEC-1 CLL line using CRISPR-Cas9 resulted in a somewhat reduced, but not abrogated effect of Mel56 suggesting effects on additional pathways beyond the BCR. Together these data provide proof-of-concept evidence for PHB inhibition as a potential strategy to target B cell lymphomas.

Alpha-synuclein (SNCA) overexpression is implicated in Parkinson’s disease (PD) pathogenesis, making SNCA downregulation a promising therapeutic strategy. We developed a SNCA -targeted epigenome therapy using an all-in-one lentiviral vector (LV) carrying deactivated CRISPR/(d)Cas9, gRNA targeted at SNCA -intron1, and either the catalytic domain of DNA-methyltransferase3A (DNMT3A), or a synthetic repressor molecule of Krüppel-associated box (KRAB)/ methyl CpG binding protein 2 transcription repression domain (MeCp2-TRD). Therapeutic efficacy was evaluated in a new PD mouse model, generated with an adeno-associated viral vector carrying an engineered minigene comprised of the human (h)A53T- SNCA expressed via the human native regulatory region. Both therapeutic vectors reduced expression of α-synuclein in the substantia nigra (SN), with LV/dSaCas9-KRAB-MeCP2(TRD) demonstrating greater repression. LV/dSaCas9-KRAB-MeCP2(TRD) also significantly reduced pathological α-synuclein aggregation and phosphorylation (Ser129), and preserved tyrosine hydroxylase expression in the SN and the striatum. Behavioral analysis following LV/dSaCas9-KRAB-MeCP2(TRD) injection, showed significant improvement in motor deficits characteristic of our PD-mouse model. Safety assessments found normal blood counts, serum chemistry, and weights. Collectively, we provide in vivo proof-of-concept for our SNCA -targeted epigenome therapy in a PD-mouse model. Our results support the system’s therapeutic potential for PD and related synucleinopathies and establish the foundation for further preclinical studies toward investigational new drug enablement.

The ability to perturb multiple proteins simultaneously within the same cell is essential for understanding and re-engineering biological pathways. CRISPR-Cas12a mutants with inactivated DNAse but intact RNAse activity (dCas12a) retain the ability to process large CRISPR RNAs (crRNAs) arrays, enabling them to target multiple genomic loci in parallel. When coupled with transcriptional effector domains, these properties make Cas12a a promising platform for multi-locus transcriptional perturbation. However, current Cas12a-based CRISPRi systems exhibit limitations in processing of multi-crRNA arrays and transcriptional regulation. Here, we combine molecular and circuit-level engineering to develop a programmable Cas12a- based CRIPSRi system capable of strong, tunable, and simultaneous knockdown of six or more genes in a single cell without genomic DNA cleavage. We demonstrate the utility of this system by systematically perturbing a partially redundant set of Bone Morphogenetic Protein (BMP) receptors, enabling quantitative analysis of BMP signaling across diverse receptor configurations.