Centriolar satellites (CS) are ubiquitous, membrane-less organelles recognized for organelle crosstalk, plasticity, diverse functions and links to developmental and neuronal diseases. However, the molecular principles governing their assembly and regulation remain poorly understood. To address this, we developed cellular and in vitro biogenesis assays that allow spatiotemporal quantification of CS granule properties during assembly, remodeling and maintenance. Using these tools, we show that CS assemble via a hierarchical pathway initiated by PCM1 scaffold formation followed by regulated client recruitment. PCM1 intrinsically assembles into granules through multimerization, a process modulated by cytoskeleton. High-resolution imaging revealed that PCM1 and its clients occupy distinct subdomains with different compositions and dynamics, adding an additional layer of regulation. Perturbing PCM1 multimerization impaired ciliary signaling, underscoring its functional importance. Collectively, these findings define the molecular basis of CS biogenesis, establish new tools to probe their context-dependent functions, and provide a framework for understanding how CS deregulation contributes to disease. More broadly, the principles uncovered here may extend to other membrane-less organelles, explaining their specificity and plasticity.

Trafficking from the endoplasmic reticulum to the Golgi apparatus comprises the first steps toward the correct localization of 30% of eukaryotic proteins. Coat protein complexes COPII and COPI are involved in forward and retrograde transport of cargo and cargo receptors between the ER and the Golgi. Although COPII forms coated vesicles in vitro, the biogenesis, morphology and organization of transport carriers in mammalian cells is debated. We use in situ cryo-electron tomography and super-resolution fluorescence microscopy to reveal the molecular architecture of ER exit sites in human cells. We visualise ribosome-exclusion zones enriched with COPII and COPI-coated vesicles and thus resolve the debate regarding the existence of COPII coated vesicles. COPII vesicles derive from ER membranes, whereas COPI vesicles originate from the ER-Golgi intermediate compartment. We quantify coated vesicle morphology and positioning with respect to other ER exit site components, providing a molecular description of the mammalian early secretory pathway.

ABSTRACT CRISPR-Cas12a is a programmable, RNA-guided endonuclease that has revolutionized biotechnology, with applications in genome engineering and diagnostics. To induce nuclease activity, Cas12a must first interact with the target dsDNA duplex by associating with a short protospacer adjacent motif (PAM) in the sequence. In this study we have split this target duplex to create PAM-proximal and PAM-distal duplex regions, which has allowed us to regulate trans-cleavage activity when these regions are included in combination or separately. These observations on Cas12a activity led to hypotheses into the related functional mechanisms, which we have tested and that have highlighted DNA/protein interactions during Cas12a complex assembly that were not otherwise apparent. Selective destabilization of the nucleic acid complexes appears to drive greater reliance on the Cas12a protein for complex stability. We have exploited this to provide significant improvements in both structural selectivity and nucleotide specificity in PAM-proximal and PAM-distal duplex regions, respectively. The result is an architecture that shows promise as a PAM-free ultra-specific platform to resolve single nucleotide polymorphisms. GRAPHICAL ABSTRACT

Shikonin, a 1,4-naphthoquinone derivative produced by several Boraginaceae species, exhibits unique pharmacological properties and is used as a natural dye. The regulatory factors of shikonin production have been demonstrated using a cell culture system of Lithospermum erythrorhizon . Among these factors, copper is known to be the strongest enhancer of shikonin production. Although shikonin biosynthesis has been studied for over 40 years, the steps of naphthalene ring formation are still unknown, as is the reason for the effect of copper. In this study, we explored candidate genes associated with shikonin production using a PCR-select subtraction experiment. Polyphenol oxidase (PPO), a dicopper-dependent oxidoreductase, was highlighted because it showed synchronous expression with shikonin production. Transcriptome analysis of hairy roots and cultured cells of this plant revealed that, of the five PPO genes expressed in L. erythrorhizon , only PPO1 showed a strong correlation with shikonin production. Next, we generated genome-edited hairy roots of LePPO1 using CRISPR/Cas9-mediated mutagenesis to analyze its impact on shikonin derivative and other specialized metabolite production. The results showed that shikonin content was markedly reduced in all LePPO1 -ge lines. Interestingly, the content of deoxyshikonofuran, a hydroquinone derivative and shunt product that branches after GHQ-3′′-OH in the shikonin biosynthetic pathway, remained unaffected in the LePPO1 -ge lines. These findings suggest that LePPO1 participates in naphthalene ring formation and explain why a copper ion is crucial for shikonin biosynthesis.

ABSTRACT Down Syndrome (DS) is the most abundant genetic form of mental retardation. It is caused by the triplication of partial or complete human chromosome 21 (HSA21). The molecular mechanisms causing it are not fully understood. Previous studies identified “Down syndrome Critical Region” (DSCR) genes that are essential or sufficient for the development of DS. However, these studies are largely inconclusive, due, in part, to the reliance on a small number of epidemiological cases. Amyloid precursor protein ( APP ) resides on HSA21 and is triplicated in DS. APP plays a role in developmental and post-natal neurogenesis, but is not thought to be part of the DSCR. The role of APP overdose in cortical malformation and cognitive impairments in DS is unknown. Mutations in APP cause familial Alzheimer’s disease (FAD). However, whether APP overdose is sufficient for the development of Alzheimer’s disease (AD) in DS is not fully understood. Here, we addressed the role of APP overdose in neuronal development and AD pathology. Using CRISPR/Cas9 gene editing, we eliminated one copy of APP from Down Syndrome-derived induced iPSCs DS APP(+/+/-) and examined the effect on neurogenesis, AD-related pathology and the expression levels of genes on HSA21 that are implicated in DS, neurodegeneration and inflammation.

Gene knock-in therapy has the potential to cure inherited liver diseases but is limited by low efficiency and delivery complexity. Here, we developed a single adeno-associated virus (AAV) vector system comprising a compact CRISPR effector, enAsCas12f, a guide RNA, and a donor template to enable therapeutic genome editing via non-homologous end joining (NHEJ). We targeted the system to the murine Alb locus and applied it to mouse models of hemophilia B, protein C (PC) deficiency, and ornithine transcarbamylase (OTC) deficiency. NHEJ-mediated knock-in showed higher efficiency than homology-directed repair, with successful therapeutic gene insertion in both neonatal and adult mice. The strategy restored plasma factor IX activity in hemophilia B ( F9 −/− ) mice, prolonged survival of PC-deficient ( Proc −/− ) mice, and prevented hyperammonemia and weight loss in OTC-deficient ( Otc spf-ash ) mice upon high protein challenge. Importantly, gene integration was restricted to the liver, with no evidence of germline transmission. This compact, all-in-one AAV knock-in platform simplifies vector production, enables efficient delivery, and achieves reliable transgene expression in vivo . Our findings highlight the potential of liver-targeted knock-in genome editing as a transplant-independent treatment for neonatal-onset metabolic diseases, offering a clinically feasible path towards curative gene therapies for a wide range of monogenic liver disorders.

Summary Background 4-1BB (CD137), a member of the TNF receptor superfamily, is a critical co-stimulatory receptor for CD8⁺ T cell activation and regulatory T cell (Treg) expansion. While its ligand 4-1BBL is typically expressed by professional antigen-presenting cells, several carcinomas also express 4-1BBL, though its function in the tumor microenvironment remains poorly defined. Methods We analyzed 4-1BBL expression across human tumors and found papillary renal cell carcinoma (pRCC) to exhibit the highest levels. Using The Cancer Genome Atlas, we found high 4-1BBL expression correlated with poor overall survival in pRCC. To study its role in vivo, we established an orthotopic humanized mouse model of pRCC by grafting ACHN cells into the renal capsule of mice reconstituted with human CD34⁺ hematopoietic stem cells. We then performed CRISPR-mediated deletion of 4-1BBL in tumor cells, followed by flow cytometry and single-cell RNA sequencing of tumor-infiltrating immune cells. Results Loss of tumor-derived 4-1BBL resulted in accelerated tumor growth and decreased immune cell clustering. In the absence of 4-1BBL, CD8⁺ T cells displayed elevated expression of PD-1, TIM-3, LAG-3, granzyme B, perforin, and NKG7, indicating a cytotoxic yet exhausted phenotype. Treg were only modestly impacted. Tumor-infiltrating CD8⁺ T cells expressed high levels of 4-1BBL and showed transcriptional signatures of altered AP-1 factors and enhanced PI3K pathway signaling. Conclusions Our findings uncover a previously unrecognized role for tumor- and T cell–derived 4-1BBL in sustaining cytotoxic CD8⁺ T cell functionality and limiting their exhaustion. This reveals a potential immune-regulatory axis that could be exploited for therapeutic modulation in renal cell carcinoma.

Johanson-Blizzard Syndrome (JBS) is an autosomal recessive spectrum disorder associated with the UBR-1 ubiquitin ligase that features developmental delay including motor abnormalities. Here, we demonstrate that C. elegans UBR-1 regulates high-intensity locomotor behavior and developmental viability via both ubiquitin ligase and scaffolding mechanisms. Super-resolution imaging with CRISPR-engineered UBR-1 and genetic results demonstrated that UBR-1 is expressed and functions in the nervous system including in pre-motor interneurons. To decipher mechanisms of UBR-1 function, we deployed CRISPR-based proteomics using C. elegans which identified a cadre of glutamate metabolic enzymes physically associated with UBR-1 including GLN-3, GOT-2.2, GFAT-1 and GDH-1. Similar to UBR-1, all four glutamate enzymes are genetically linked to human developmental and neurological deficits. Proteomics, multi-gene interaction studies, and pharmacological findings indicated that UBR-1, GLN-3 and GOT-2.2 form a signaling axis that regulates glutamate homeostasis. Developmentally, UBR-1 is expressed in embryos and functions with GLN-3 to regulate viability. Overall, our results suggest UBR-1 is an enzyme hub in a GOT-2.2/UBR-1/GLN-3 axis that maintains glutamate homeostasis required for efficient locomotion and organismal viability. Given the prominent role of glutamate within and outside the nervous system, the UBR-1 glutamate homeostatic network we have identified could contribute to JBS etiology.

Toxoplasma and other Apicomplexan parasites, switch between different developmental stages to persist in and transmit between hosts. Toxoplasma can alternate between systemic tachyzoites and encysted bradyzoite forms found in the CNS and muscle tissues. How parasites sense these tissue types and trigger differentiation remains largely unknown. We show that Toxoplasma differentiation is induced under glucose-limiting conditions and using a CRISPR screen identify parasite genes required for growth under these conditions. From ∼25 identified genes important for differentiation we show that lactate and glutamine metabolism is linked to differentiation and demonstrate the importance of an E3 ubiquitin ligase complex, orthologous to glucose induced degradation deficient (GID) complex in yeast and CTLH complex in humans. We show that TgGID likely regulates translational repression of a key transcription factor required for differentiation, BFD1, through its 3’ utr. Overall, this work provides important new insight into how these divergent parasites sense different host cell niches and trigger stage conversion through a ubiquitination-dependent program.

Abstract It was recently shown that inhibition of polo-like kinase 4 (PLK4) induces TP53 -dependent synthetic lethality in cancers with chromosome 17q-encoded TRIM37 copy number gain due to cooperative regulation of centriole duplication and mitotic spindle nucleation. We show here that chromosome 17q/TRIM37 gain is a pathognomonic feature of high-risk neuroblastoma and renders patient-derived cell lines hypersensitive to the novel PLK4 inhibitor RP-1664. We demonstrate that centriole amplification at low doses of RP-1664 contributes to this sensitivity in a TRIM37 - and TP53 -independent fashion. CRISPR screens and live cell imaging reveal that upon centriole amplification, neuroblastoma cells succumb to multipolar mitoses due to an inability to cluster or inactivate supernumerary centrosomes. RP-1664 showed robust anti-tumor activity in 14/15 neuroblastoma xenograft models and significantly extended survival in a transgenic murine neuroblastoma model. These data support biomarker-directed clinical development of PLK4 inhibitors for high-risk neuroblastoma and other cancers with somatically acquired TRIM37 overexpression.

Abstract Despite initial responses, most patients with metastatic lung cancer—including those with EGFR mutations—ultimately develop resistance to targeted therapies. To systematically uncover mechanisms underlying this resistance, genome-wide CRISPR knockout and activation screens were conducted in EGFR-mutant lung cancer cell lines treated with EGFR inhibitors such as osimertinib and gefitinib. These screens highlighted a recurrent involvement of genes associated with the Hippo signaling pathway. Notably, a subset of tumor cells, termed 'persister' cells, survive initial osimertinib exposure by engaging non-genetic, transcriptional adaptation mechanisms that promote drug tolerance. Our studies, integrating both genetic and pharmacological approaches, identified Hippo pathway activation as a key driver of this drug-tolerant state. Importantly, co-inhibition of EGFR and the Hippo signaling axis led to a pronounced reduction in cell viability in both established cell lines and patient-derived organoids. These findings propose that dual targeting of EGFR and Hippo signaling may offer a promising therapeutic approach to overcome resistance in EGFR-mutant lung cancer.

Objectives: To explore the molecular chemistry and structural biology of bacteriophages as precision-guided therapeutic agents. This review reframes phages as programmable nanomachines governed by defined chemical interactions, focusing on their relevance to antimicrobial resistance, targeted lysis, and synthetic modification. Materials and Methods: A systematic review was conducted using recent peer-reviewed literature from PubMed, Scopus, and Google Scholar, covering bacteriophage structural biology, enzymatic lysis mechanisms, chemical modifications, genomic annotation, and bioengineering techniques. Studies were selected based on relevance to molecular chemistry, nanotechnology, and therapeutic development. Results: Bacteriophages demonstrate ligand-specific host recognition, capsid-mediated genome packaging, and enzymatic lysis using holins and endolysins. Advances in PEGylation, surface conjugation, and CRISPR engineering have expanded their therapeutic potential. Genomic tools now enable personalized phage matching, while hybrid phage-nanoparticle systems enhance targeting and delivery. Conclusions: Phages can be rationally designed as chemically programmable antimicrobials. Their structure–function relationship, enzymatic precision, and genomic adaptability position them as promising agents in the fight against multidrug-resistant pathogens. Integration of chemistry, bioinformatics, and synthetic biology enables development of next-generation phage therapeutics.

Abstract Functional genomics has been hampered by the paucity of efficient methods that connect genotype and metabolic phenotype at single-cell resolution. Using the industrial microalga Nannochloropsis oceanica as a model, we introduced a platform that comprises a genome-wide single-gene-edited mutant library and high-throughput Raman-activated Cell Sorting (RACS). The CRISPR/Cas-generated library consists of 3,567 microalgal mutants derived from 2,397 effective guide RNAs. Label-free sorting of the library for high carotenoid content by RACS unravels mutations in the violaxanthin de-epoxidase ( noVDE ) or in the proteasome assembly chaperone 4 ( noPAC4 ) genes. Knocking out all five known noVDE s reveal that the high carotenoid content is due to violaxanthin increase, whilst noPAC4 knockout boosted carotenoid content with elevations in violaxanthin, zeaxanthin, and β-carotene. Genetic and transcriptomic evidences suggest two previously unknown modes of carotenogenesis regulation mediated by noPAC4: epigenetic mechanisms via histone deacetylase (HDAC) and post-translational controls by the 26S proteasome. Therefore, by label-freely sorting single-cell metabolic phenotype and rapidly yet unambiguously tracing it to a genotype, this new forward-genetics approach can greatly accelerate the discovery of new genes and pathways.

Abstract Cancer therapy faces a critical need for treatments that selectively eliminate malignant cells without harming healthy tissue. The Proteus Project addresses this challenge by engineering a programmable gene circuit that couples CRISPR-based RNA sensing with an inducible cell death mechanism. Specifically, we repurpose a novel Type III-E CRISPR-Cas system (“Craspase”) – an RNA-guided protease complex – to detect cancer-specific RNA transcripts and, in response, cleave engineered gasdermin fusion proteins to trigger cell death (1)(2). We constructed the Proteus system in Saccharomyces cerevisiae as a surrogate model, integrating components that sense an oncogenic KRAS mutation and execute targeted pyroptosis (inflammatory apoptosis-like cell death). Preliminary results demonstrate successful assembly of the Craspase– gasdermin circuit, expression of key proteins, and proof-of-concept cell killing specifically in the presence of the oncogenic RNA trigger. This work, conducted as part of the iGEM 2025 SynBio Collective, showcases a modular synthetic biology approach for precision oncology therapeutics. The ongoing study underscores the potential of CRISPR-guided proteases in in situ cancer cell ablation and sets the stage for future validation in mammalian systems.

ABSTRACT CTCF-mediated chromatin loops are known to influence gene regulation, yet their role in pre-mRNA splicing remains incompletely understood. Here, we demonstrate that structural variants (SVs) at the anchors of intronic CTCF loops can modulate exon usage. By integrating high-resolution three-dimensional (3D) genome organization and gene expression datasets from C57BL/6J (B6) and 129S1/SvImJ (129S) mouse embryonic stem cells (ESCs), with structural variant (SV) maps from the 129S mouse, we identified thousands of intron-anchored CTCF loops. Our data indicate that SVs intersecting loop anchors are more frequently associated with differential exon inclusion events than with changes in overall gene expression. CRISPR/Cas9 deletion of two SV-harboring intronic CTCF sites in Numbl and Ireb2 validated the predicted splicing shifts observed between B6 and 129S ESC that correspond with diminished long-range chromatin looping. Our findings reveal a direct mechanistic link between 3D genome architecture and alternative splicing and highlight non-coding SVs as modulators of transcript diversity. Our study has thus identified a novel class of CTCF-bound regulatory elements regulating alternative splicing. Cataloging and validating these functional elements will elucidate molecular mechanisms underlying phenotypic variation within populations.

CHARGE syndrome is a developmental disorder that affects 1 in 10,000 births, and patients exhibit both physical and behavioral characteristics. De novo mutations in CHD7 (chromodomain helicase DNA binding protein 7) cause 67% of CHARGE syndrome cases. CHD7 is a DNA-binding chromatin remodeler with thousands of predicted binding sites in the genome, making it challenging to define molecular pathways linking loss of CHD7 to CHARGE phenotypes. To address this problem, here we used a previously characterized zebrafish CHARGE model to generate transcriptomic and proteomic datasets from larval zebrafish head tissue at two developmental time points. By integrating these datasets with differential expression, pathway, and upstream regulator analyses, we identified multiple consistently dysregulated pathways and defined a set of candidate genes that link loss of chd7 with disease-related phenotypes. Finally, to functionally validate the roles of these genes, CRISPR/Cas9-mediated knockdown of capgb , nefla , or rdh5 phenocopies behavioral defects seen in chd7 mutants. Our data provide a resource for further investigation of molecular mediators of CHD7 and a template to reveal functionally relevant therapeutic targets to alleviate specific aspects of CHARGE syndrome. Summary Statement We have identified Chd7 target genes capgb , nefla , and rdh5 that mediate CHARGE model phenotypes from transcriptomic and proteomic analysis of chd7 wild type, heterozygous, and homozygous mutant zebrafish brain tissue at two developmental time points.

Chimeric antigen receptor (CAR) T-cell therapy has transformed the treatment of hematologic cancers. However, its efficacy in solid tumors, including pancreatic ductal adenocarcinoma (PDAC), has been limited. By integrating modular CRISPR screening with immunocompetent orthotopic models of PDAC, we identified unknown tumor-intrinsic modulators of CAR T-cell therapy response. Disruption of genes involved in oxidative and proteotoxic stress, particularly the Nrf2 target Slc33a1 , sensitizes PDAC tumors to CAR T-cell killing. Single cell gene expression analyses revealed that CAR-T resistant tumors exhibit reduced Nrf2 pathway activity. Mechanistically, we show that Nrf2 pathway hyperactivation by genetic ablation of Keap1 or expression of a tumor-derived Keap1 allele sensitized PDAC tumors to CAR T-cell therapy. Thus, cell-intrinsic molecular states accompanying malignant progression can sensitize tumor cells to cell-based immunotherapies. These molecular mechanisms could be exploited to augment both the efficacy of CAR-T cell therapy in solid malignancies, and may allow patient stratification by tumor genotype. Statement of significance CAR T-cell therapy remains an unsolved challenge for pancreatic cancer. The discovery of tumor-intrinsic mechanisms of resistance has been largely limited by current experimental models. Using large-scale genomic screening in an orthotopic, immunocompetent model of pancreatic cancer, we uncover a role for cell-intrinsic metabolic states in regulating CAR T-cell response.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterised by motor neuron deterioration. Genetic factors play a significant role in all cases, with 15 genome-wide significant study (GWAS) risk loci identified to date. Follow-up of these loci is a powerful strategy for research translation, as drug targets supported by genetic evidence are more likely to succeed in clinical development. Here, we focus on the RPSA-MOBP locus on chromosome 3 (lead SNP, rs631312, OR = 1.08 95% CI: 1.06–1.10, p = 3.3 × 10⁻¹²). We employ integrative in silico analyses to prioritise candidate genes, combining multiple ‘omics-based approaches, including Functional Mapping and Annotation (FUMA), Polygenic Priority Scoring (PoPS), Transcriptome-Wide Association across/within tissues (TWAS), gene-based test (mBAT-combo), chromatin interaction mapping (H-MAGMA), and Summary data Mendelian Randomisation (SMR), with GWAS data ( N cases = 29,612, N controls = 122,656). Both RPSA and MOBP were prioritised as candidate genes in multiple analyses. In-vivo expression analyses in ALS blood or iPSC-motor neurons were unremarkable for these genes but also other-relevant ALS genes. RPSA , highly conserved in zebrafish (92% homology), was selected for functional modelling, noting previously generated Mobp -ko mice show minimal phenotypic changes. CRISPR/Cas9-induced rpsa loss-of-function (LOF) in zebrafish triggers progressive and severe phenotypes mimicking pathology observed in SMN- and TDP43-deficient zebrafish, two key proteins/genes associated with diseases of the motor neurons. RPSA -deficient animals exhibit marked motor neuron axon pathology, progressive loss of motor function and rapid decline culminating with premature death at around 7 days- post-fertilisation. These phenotypes were notably similar to those observed in SMN and TDP-43 zebrafish models, together with prominent cardiovascular abnormalities. This study identifies RPSA as a critical gene for motor neuron health, with implications for ALS pathogenesis. The RPSA/MOBP locus is also associated with other neurodegenerative diseases including frontotemporal dementia/FTD, corticobasal degeneration/CBD and progressive supranuclear palsy/PSP, highlighting its potential as a therapeutic target for multiple conditions.

TRIB members (TRIB1, TRIB2 and TRIB3) represent atypical members of the serine/threonine kinase superfamily and are involved in multiple biological processes such as cell proliferation and differentiation. TRIB roles in GC are not fully investigated. We hypothesized that TRIB members play crucial roles in regulating GC activity and may activate separate signaling pathways. TRIB1 and TRIB3 are induced in GC of ovulatory follicles (OF) following hCG injection as compared to dominant follicles (DF) whereas TRIB2 is suppressed by hCG in OF. Protein analyses of cultured primary GC showed that luteinizing hormone (LH) treatment inhibited TRIB2 and induced TRIB3, while follicle-stimulating hormone (FSH) treatment increased TRIB2 and TRIB3 expression but at different times. These results demonstrate a different regulation of TRIB members during follicular development and in response to gonadotropins. TRIB3 inhibition via CRISPR/Cas9 showed a positive effect on AKT signaling pathway while showing negative effects on P38 MAPK signaling. Overall, TRIBs may play crucial roles in regulating GC function and activity and may activate separate signaling pathways, which impact follicular development, ovulation and luteinization.

Foodborne pathogens represent a class of pathogenic microorganisms capable of causing food poisoning or serving as foodborne vectors, constituting a major source of food safety concerns. With increasing demands for rapid diagnostics, conventional culture-based methods and PCR assays face limitations due to prolonged turnaround times and specialized facility requirements. While CRISPR-based detection has emerged as a promising rapid diagnostic platform, its inherent inability to detect low-abundance targets necessitates coupling with isothermal amplification, thereby increasing operational complexity. In this study, we developed a novel amplification-free Cascade-CRISPR detection system utilizing hairpin DNA amplifier. This method achieves detection sensitivity as low as 10 fM for DNA targets within 30 minutes without requiring pre-amplification, with background signal suppression achieved through optimized NaCl concentration. Validation using artificially contaminated food samples demonstrated the platform's robust performance for both Toxoplasma gondii(T. gondii) and Listeria monocytogenes(L. monocytogenes) detection, confirming broad applicability. In summary, this study establishes an amplification-free Cascade-CRISPR detection platform that achieves high sensitivity and rapid turnaround, demonstrating strong potential for on-site screening of foodborne pathogens.

Interactions between drugs and their targets impact efficacy and, when altered by mutation, can result in resistance 1-3 . Assessing and understanding the impacts of all possible mutations at a drug binding site remain challenging, however 4-6 . Here, we used Multiplex Oligo Targeting (MOT) for mutational profiling, and computational modelling, to decode efficacy and resistance space at the otherwise native binding site for a low nanomolar potency, anti-trypanosomal, proteasome inhibitor 7 . We saturation-edited twenty codons in the Trypanosoma brucei proteasome β5 subunit and subjected the resulting MOT libraries to stepwise drug selection. Amplicon sequencing, and codon variant scoring, yielding dose-response profiles for >100 resistance-conferring mutants, among 1,280 possible codon variants. Codon variant scores were predictive of relative resistance observed using a bespoke set of mutants, while fitness profiling revealed otherwise extensive constraints on mutational fitness and resistance space. The resistance profile that emerged allowed us to readily predict routes to spontaneous drug resistance observed within ‘accessible’, single nucleotide mutational space. In silico analysis of β5 subunit mutations predicted impacts on ligand affinity via steric effects, hydrogen-bonding and lipophilicity, which when combined with predictions of proteasome function perturbing mutations, were closely aligned with observed impacts on drug resistance. We conclude that MOT-library profiling facilitates assessment of all possible mutations at a drug binding site. Further decoding of drug target structure-activity relationships and drug resistance space will facilitate the design of more effective and durable drugs.

ABSTRACT Since their discovery, CRISPR–Cas systems have been widely applied in areas ranging from genome editing to biosensing, owing to their specific, RNA-guided target recognition. Their performance in complex biological environments has been extensively studied, particularly to optimize guide RNA design and minimize off-target cleavage. Here, we focus on the kinetic inhibition of the interaction between Cas12a - a Class 2, Type V effector - and its target, caused by interference from non-cognate background nucleic acids. This effect is particularly relevant for sensing applications in complex mixtures or cellular contexts, where genome- and transcriptome-derived sequences may impede CRISPR–Cas activity. Using in vitro assays under defined conditions, we systematically examine the influence of background single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) on reaction kinetics. We find that both the purine-to-pyrimidine ratio and the GC content of the guide RNA seed region significantly affect kinetic inhibition by background polynucleotides. Guide RNAs with low GC content and a high purine fraction in the seed region were least affected by background sequences. Experiments with dCas12a-based gene activation in living cells indicate that our in vitro findings may also be relevant for in vivo applications.

Understanding toxin resistance in insects is key to appreciate niche adaptations, but remains challenging due to its often complex genetic basis. A well-known example is the specialized association of Drosophila sechellia with noni fruit ( Morinda citrifolia ), which is toxic to most other insects, including the closely-related drosophilids D. simulans and D. melanogaster . Noni toxicity is due to its high concentration of octanoic acid (OA), but the mechanisms that determine sensitivity or resistance to OA remain poorly understood. Here, we experimentally-evolved D. simulans with increased OA resistance, identifying multiple loci under selection. Cross-referencing these with a genome-wide, OA-resistance CRISPR screen in a D. melanogaster cell line highlighted two proteins: Kraken, a putative detoxification enzyme expressed in digestive and renal tissues, and Alkbh7, a mitochondrial protein linked to fatty acid metabolism. Both genes show elevated expression in D. sechellia and OA-resistant D. simulans . In D. melanogaster , kraken mutants are more OA-sensitive, while Alkbh7 overexpression increased OA resistance. Importantly, mutation of these genes in D. sechellia reduced OA tolerance. Our identification of genes underlying OA resistance in laboratory and natural contexts demonstrates how complementary, cross-species selection approaches can provide insights into toxin susceptibility and adaptation mechanisms, with practical applications in the characterization of novel insecticides.

Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacterial phage defense systems (PDSs). Here, we explore the relationship between ARGs and PDSs in a sample of 2,559 plasmids originating from 1,044 E. coli isolates, representing a snapshot of clinical and non-clinical diversity in Oxfordshire, UK (2008-2020). In total, we identify 3,193 ARGs and 14,013 PDSs (180 unique types). We demonstrate that E. coli plasmids are enriched for ARGs and PDSs (both p<0.001), with a bias towards toxin-antitoxin/abortive-infection, TIR-domain and CBASS systems (all q<0.025). We proceed to show that ARGs and PDSs are physically linked by plasmids ( p <0.001). Together, our results suggest that phage therapy may inadvertently select for antibiotic resistant bacteria, and that antibiotic use may similarly drive resistance to phage.

Ubiquitin E3 ligases play crucial roles in the DNA damage response (DDR) by modulating the turnover, localization, activation, and interactions of DDR and DNA replication proteins. To gain further insight into how the ubiquitin system regulates the DDR, we performed a CRISPR-Cas9 knockout screen focused on E3 ligases and related proteins with the DNA topoisomerase I inhibitor, camptothecin. This uncovered the CTLH ubiquitin E3 ligase complex — and particularly one of its core subunits, MAEA — as a critical regulator of the cellular response to single-ended DNA double-strand breaks (seDSBs) and replication stress. In tandem, we identified patients with variants in MAEA who present with neurodevelopmental deficits including global developmental delay, dysmorphic facial features, brain abnormalities, intellectual disability, and abnormal movement. Analysis of patient-derived cell lines and mutation modeling reveal an underlying defect in HR-dependent DNA repair and replication fork restart as a likely cause of disease. We propose that MAEA dysfunction hinders DNA repair by reducing the efficiency of RAD51 loading at sites of DNA damage, which compromises genome integrity and cell division during development.