Lacticaseibacillus rhamnosus GG (LGG) is one of the most studied probiotic strains and is widely used in both food and therapeutic industries. With its safe and health-beneficial properties, LGG is an ideal candidate for genome modification to enhance its functionalities for food, industrial and pharmaceutical applications. However, precise and efficient genome engineering tools for LGG are unavailable. In this study, we developed a novel genome engineering tool for LGG based on its endogenous type II-A CRISPR-Cas9 system. By employing a validated protospacer adjacent motif (PAM), a customized single guide RNA (sgRNA) expression cassette and a homologous repair template, we successfully reprogrammed the native CRISPR-Cas9 system for targeted genome modifications. Using this method, we successfully constructed a fucose-negative LGG incapable of growing on L-fucose and a lactose-positive LGG. The lactose-positive LGG exhibited significantly improved growth in milk compared to its parental strain LGG, which is unable to ferment lactose, attributed to its ability to metabolize lactose efficiently. Moreover, this strain showed robust growth during yogurt fermentation and maintained viability during cold storage for at least three weeks. These findings highlight the potential of the lactose-positive LGG as an improved culture for dairy industry and a functional probiotic for food and therapeutic applications. Importance A precise and efficient genome editing tool is essential for unlocking the full potential of Lacticaseibacillus rhamnosus GG (LGG), the most extensively studied probiotic strain. This study established the first high-efficiency genome editing platform for LGG by harnessing the endogenous type II-A CRISPR-Cas9 system. Using this tool, we achieved targeted gene modifications, without introducing scars, heterologous DNA, or antibiotic resistance genes. The engineered lactose-positive LGG strain demonstrated improved growth in lactose-containing dairy products and robust performance during yogurt fermentation, highlighting its industrial and therapeutic value. This platform not only advances the development of enhanced probiotic strains but also establishes LGG as a versatile vehicle for synthetic biology and biotechnological applications.

Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, viruses of bacteria, are drivers of gut bacterial composition in the human gut and could affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore the direct interactions occurring between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. A total of 1,086 bifidobacterial genomes were analysed in this study, revealing complex systems to prevent viral invasion. Despite their characteristically small genomes, Bifidobacterium strains harboured more than double the number of defence systems as most bacteria. In total, 34 defence system types and 56 subtypes were detected, including several different CRISPR-Cas systems with spacers that targeted almost three-quarters of bifidobacteria-derived prophages. We identified at least one prophage which met our stringent quality control measures in ~63% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. Additionally, prophages were found to encode various anti-defence systems, such as anti-CRISPR genes and restriction modification resistance mechanisms. In summary, our investigation reveals "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.

Congenital heart defects (CHDs) occur in about 1% of live births and are the leading cause of infant death due to birth defects. While there have been remarkable efforts to pursue large-scale whole-exome and genome sequencing studies on CHD patient cohorts, it is estimated that these approaches have thus far accounted for only about 50% of the genetic contribution to CHDs. We sought to take a new approach to identify genetic causes of CHDs. By combining analyses of genes that are under strong selective constraint along with published embryonic heart transcriptomes, we identified over 200 new candidate genes for CHDs. We utilized protein-protein interaction (PPI) network analysis to identify a functionally-related subnetwork consisting of known CHD genes as well as genes encoding proteasome factors, in particular POMP , PSMA6 , PSMA7 , PSMD3 , and PSMD6 . We used CRISPR screening in zebrafish embryos to preliminarily identify roles for the PPI subnetwork genes in heart development. We then used CRISPR to create new mutant zebrafish strains for two of the proteasome genes in the subnetwork: pomp and psmd6 . Phenotypic analyses confirm critical roles for pomp and psmd6 in heart development. In particular, we find defects in myocardial cell shapes and in outflow tract development in pomp and psmd6 mutant zebrafish embryos, and these phenotypes have been observed in other zebrafish CHD-gene mutants. Our study provides a novel systems genetics approach to further our understanding of the genetic causes of human CHDs. Author Summary Congenital heart defects (CHDs) are birth defects resulting in the abnormal structure and function of the heart. Genetic mutations are a significant cause of CHDs. Many studies have used genome sequencing of CHD patients and their families to gain knowledge of the mutations that cause CHDs. However, these studies have only found about 50 percent of the genes involved in CHDs. Here, we take a new approach to identifying genes that are required for heart development and that may cause CHDs, generating a list of over 200 candidate genes. Using multiple data systems, including human exome sequences, mouse transcriptomes, and protein-protein interactions, we identify a small group of related potential CHD genes that includes multiple genes encoding proteasome factors. These factors are known to be important for assembling the proteasome, a large molecular machine that eliminates unneeded or damaged proteins from the cell, but which has not been shown to contribute to CHD. We use a CRISPR-based approach in zebrafish to specifically eliminate some of these candidate genes and reveal new roles for proteasome genes in heart development. We show that loss of proteasome gene functions leads to zebrafish heart defects that resemble those seen in other zebrafish CHD-gene mutants. This study shows that a proteasome gene family contributes to heart development, advancing our understanding of the causes of CHDs. By increasing our understanding of the genetic causes of CHDs, our work should lead to better screening, more accurate diagnoses, and, ultimately, better treatments for these disorders.

The evolutionary arms race between bacteriophages and their bacterial hosts has driven the evolution of sophisticated adaptive immune systems, such as CRISPR-Cas, as a crucial defense mechanism. While bacteriophages have developed various anti-CRISPR strategies to counteract these immune systems, the role of bacterial host factors in enhancing CRISPR-Cas functions has been relatively unexplored. In this study, we employ an artificial intelligence (AI)-driven approach to systematically analyze potential interactions between Escherichia coli ( E. coli ) proteins and fifteen previously uncharacterized Cas12 proteins, generating 65,715 predicted binary complex structures. Our findings reveal a previously unknown dimension of CRISPR immunity, demonstrating that the host’s ubiquitous redox enzyme, thioredoxin (TrxA), significantly enhances the DNA cleavage efficiency of a phage-encoded, miniature Cas12 nuclease (termed ‘Cas12 hacker’). This synergistic relationship represents a strategic inversion, where a bacteriophage hijacks a host protein to reinforce its own genome degradation machinery, possibly targeting rival nucleic acids. Through comprehensive biochemical characterizations, structural analyses of the Cas12 hacker-TrxA-sgRNA-dsDNA quaternary complex, and in vivo bacterial defense assays, we uncover an intricate association in which thioredoxin binds to and activates the Cas12 hacker nuclease, intensifying its DNA cleavage capacity and bolstering CRISPR immunity. Our findings expand the understanding of the molecular interactions underlying host-phage conflicts and highlight the potential for harnessing endogenous host factors to enhance the capabilities of CRISPR-based genetic engineering tools.

A 2-year-old Large White research gilt was presented to the Comparative Theriogenology service at WSU for infertility. She was produced from the transfer of genetically modified embryos obtained by in vitro fertilization (IVF) that had been treated with CRISPR-Cas9 reagents to mutate the NANOS2 gene. Since birth, the gilt showed a so-called “skyhook” vulva and abnormal estrous cycles. She was artificially inseminated multiple times, starting at 5 months of age, with semen from a proven boar, but never conceived. On transabdominal ultrasonography of the reproductive tract, a unilateral ovotestis was suspected. An exploratory laparotomy was performed and confirmed the presence of ovarian and testicular tissue on her right gonad. The diagnosis was confirmed by histology following unilateral gonadectomy. The cytogenic evaluation revealed the gilt to be XX, 38; SRY-negative. The gilt showed estrus signs 4 months after surgery, and artificial insemination was performed, which resulted in a pregnancy. She delivered six piglets. Necropsy was performed following humane euthanasia. Several abnormalities of the reproductive tract were discovered, including a unilateral mucometra due to a complete septum preventing communication between the right uterine horn and the body of the uterus. This case is novel because it demonstrates that surgical removal is an effective treatment for fertility in SRY-negative XX DSD gilts with partial masculiniza-tion, posing the presence of a normal ovary and a developed oviduct and uterine horn.

ABSTRACT Background/Purpose Desmoplakin (DSP) mutations are linked to familial cardiomyopathies with a very high arrhythmogenic propensity. While autosomal recessive inheritance forms manifest in the cardio-cutaneous Carvajal syndrome, the dominant-inheritance variants associate to DSP-cardiomyopathy (DSP-CM). This latter is a subtype of Arrhythmogenic Cardiomyopathy characterized by frequent myocarditis-like episodes, dominant left ventricular (LV) remodeling, recurrent premature ventricular contractions and life-threatening arrhythmias, frequently preceding LV dysfunction and dilation. Notably, DSP-CM evades the diagnostic identifiers of Arrhythmogenic Cardiomyopathy, further complicating risk-stratification and prediction. At the time being, the pathogenetic mechanisms underlying DSP-related cardiomyopathies are largely obscure and their elucidation is urgently required. Methods To this end, we employed CRISPR-Cas9 to generate a novel knock-in mouse model harboring a point mutation at the murine ortholog of human Serine-299, a mutation site previously identified in a family affected by left dominant-Arrhythmogenic Cardiomyopathy. In both heterozygotes and homozygotes, cardiac function was assessed by echocardiography and telemetry-ECG, at different ages. Results were correlated with heart structure, which was assessed by ultrastructural, histopathological and molecular/biochemical assays. The effects of moderate exercise on disease manifestations were tested. Results The homo- and hetero-zygous expression of mutant Dsp S311A allele replicated the human cardiac phenotypes of Carvajal syndrome and DSP-CM, respectively. Indeed, Dsp S311A/S311A mice featured precocious dilated cardiomyopathy with biventricular fibrotic remodeling, aneurisms, systolic dysfunction, increased arrhythmic vulnerability, sudden death and, remarkably, cutaneous defects. Differently, Dsp WT/S311A mice did not show evident cutaneous alterations, and myocardial remodeling and contractile dysfunction developed later and were associated to increased cell death, inflammatory response and patchy fibrosis predominantly in the LV. Notably, as observed in certain patient subgroups, Dsp WT/S311A mice had electrophysiological alterations (i.e. QRS prolongation, distal conduction defects and sustained ventricular arrhythmias) prior to developing contractile dysfunction. Furthermore, in both genotypes, exercise accelerated myocardial remodeling and increased the incidence of arrhythmic mortality. Conclusions Our novel Dsp S311A mice recapitulate the clinical and pathological features of the respective dominant (i.e. DSP-CM) and recessive (i.e. Carvajal syndrome) forms of DSP-related cardiomyopathies. Thus, Dsp S311A mice are a novel experimental model of human diseases, suited to test therapeutic interventions aimed at reducing the burden of stress-dependent SD.

Nearly all mitochondrial proteins are imported into mitochondria from the cytosol. How nascent mitochondrial precursors acquire and sustain import-competence in the cytosol under normal and stress conditions is incompletely understood. Here, we show that under normal conditions, the Hsc70 and Hsp90 systems interact with and redundantly minimize precursor degradation. During acute import stress, Hsp90 buffers precursor degradation, preserving proteins in an import-competent state until stress resolution. Unexpectedly, buffering by Hsp90 relies critically on a mitochondrial targeting signal (MTS), the absence of which greatly decreases precursor-Hsp90 interaction. Site-specific photo-crosslinking and biochemical reconstitution showed how the MTS directly engages co-chaperones of Hsc70 (St13 and Stip1) and Hsp90 (p23 and Cdc37) to facilitate chaperone retention on the mature domain. Thus, the MTS has a previously unappreciated role in regulating chaperone dynamics on mitochondrial precursors to buffer their degradation and maintain import competence, functions that may facilitate restoration of mitochondrial homeostasis after acute import stress. Significance statement Mitochondrial proteins encoded by the nuclear genome are synthesized in the cytosol before their subsequent import into mitochondria. The factors that recognize mitochondrial precursors in the cytosol to maintain their import-competence are incompletely defined. Using a systematic site-specific photo-crosslinking strategy, the authors find that the mitochondrial targeting signal (MTS) is directly recognized by co-chaperones of Hsc70 and Hsp90. The co-chaperones facilitate recruitment, retention, and remodeling of these general chaperones on the nascent precursor protein. Chaperone retention becomes particularly important during mitochondrial stress, when precursors must avoid degradation during a prolonged period in the cytosol.

Many cancers use an alternative lengthening of telomeres (ALT) pathway for telomere maintenance. ALT telomeric DNA synthesis occurs in ALT telomere-associated PML bodies (APBs). However, the mechanisms by which APBs form are not well understood. Here, we monitored the formation of APBs with time-lapse imaging employing CRISPR knock-in to track the promyelocytic leukemia (PML) protein at endogenous levels. We found APBs form via two pathways: telomeres recruit PML proteins to nucleate PML bodies de novo, or telomeres fuse with preformed PML bodies. Both nucleation and fusion of APBs require interactions between SUMO and SUMO interaction motifs (SIMs). Moreover, APB nucleation is associated with higher levels of SUMOs and SUMO-mediated recruitment of DNA helicase BLM, resulting in more robust telomeric DNA synthesis. Finally, further boosting SUMO levels at telomeres enhances APB nucleation, BLM enrichment, and telomeric DNA synthesis. Thus, high SUMO levels at telomeres promote APB formation via nucleation, resulting in stronger ALT activity.

Experimental studies suggest that the probiotic yeast Saccharomyces boulardii can mitigate the symptoms of inflammatory bowel disease. However, these results are equivocal and S boulardii probiotic therapy has not gained widespread acceptance in clinical practice. To assess whether the therapeutic properties of S boulardii might be improved upon, we engineered S boulardii to overproduce and secrete spermidine, a pro-regenerative natural metabolite. We employed CRISPR gene deletion and transposon-mediated gene integration to manipulate expression of key enzymes in the polyamine synthetic and transport pathways. We tested the engineered yeast by oral gavage of mice treated with azoxymethane and dextran sulfate sodium to induce chronic colitis and colon cancer. We demonstrate that oral delivery of spermidine-secreting S boulardii in mice populates the gastrointestinal tract with viable spermidine-secreting S boulardii cells and raises free spermidine levels in the gastrointestinal tract. Strikingly, spermidine-secreting S boulardii strains were significantly more effective than wild-type S boulardii in reducing dextran sulfate sodium-induced colitis as well as colitis-associated colon cancer in mice. These results suggest that in situ spermidine secretion by engineered synthetic biotic yeast strains may be an effective and low-cost therapy to mitigate inflammatory bowel disease and colon cancer.

Background FZD8 could be a promising therapeutic target in osteoporosis (OP), although the signal transduction mechanism in OP regarding FZD8 has not been completely elucidated. Aims We used the CRISPR/Cas9 technique to develop an Fzd8 -knockout mouse model to study whether Fzd8 inactivation results in genetic changes with potential correlations to OP. Materials and Methods Genotypes of distinguished classified knockout mice, i.e., heterozygous, homozygous, and wild-type were identified through PCR. Applying the murine model, third generation mice were used for the downstream experiments. We investigated the potential relevance of differentially expressed genes (DEGs) in OP. Results We found that osteoclasts significantly increased in Fzd8 -knockout homozygous mice, compared to wild-type mice, while osteoblasts reduced significantly. Before transcription, heterozygous and homozygous mice possessed DEGs related to exons SNP, which are associated with exons CNV. After transcription, DEGs related to exons SNP in heterozygous and homozygous mice were observed, some of which are potentially associated with OP based on pathway and gene set enrichment analyses. Conclusions Our Fzd8- knockout murine model showed that there were significant alternations in Fzd10 and Lta gene expressions and Itgb3 and RANK protein expressions among the wild-type and homozygous mice, which are significantly associated with bone remodeling. Our results revealed that FZD8 could be a therapeutic target in OP. This study elucidates the molecular mechanisms in OP, providing evidence-based data for OP drug development and treatment.

The impact of cancer driving mutations in regulating immunosurveillance throughout tumor development remains poorly understood. To better understand the contribution of tumor genotype to immunosurveillance, we generated and validated lentiviral vectors that create an epi-allelic series of increasingly immunogenic neoantigens. This vector system is compatible with autochthonous Cre-regulated cancer models, CRISPR/Cas9-mediated somatic genome editing, and tumor barcoding. Here, we show that in the context of KRAS-driven lung cancer and strong neoantigen expression, tumor suppressor genotype dictates the degree of immune cell recruitment, positive selection of tumors with neoantigen silencing, and tumor outgrowth. By quantifying the impact of 11 commonly inactivated tumor suppressor genes on tumor growth across neoantigenic contexts, we show that the growth promoting effects of tumor suppressor gene inactivation correlate with increasing sensitivity to immunosurveillance. Importantly, specific genotypes dramatically increase or decrease sensitivity to immunosurveillance independently of their growth promoting effects. We propose a model of immunoediting in which tumor suppressor gene inactivation works in tandem with neoantigen expression to shape tumor immunosurveillance and immunoediting such that the same neoantigens uniquely modulate tumor immunoediting depending on the genetic context. One Sentence Summary Here we uncover an under-appreciated role for tumor suppressor gene inactivation in shaping immunoediting upon neoantigen expression.

In Atlantic salmon ( Salmo salar ), infectious salmon anemia virus (ISAV) and infectious pancreatic necrosis virus (IPNV) evade host immune response through complex antagonistic mechanisms. Type I interferons (IFNs) play a pivotal role in antiviral defense by signaling through heterodimeric receptors to activate the JAK-STAT pathway and drives the expression of interferon-stimulated genes (ISGs). In this study, CRISPR-Cas9 was used to knock out (KO) interferon receptor genes ( crfb1a , crfb5a , il10rb , ifngr2a ) and a combined group of candidate receptors ( crfb1a , crfb5a , il10rb , ifngr2a , il10r2 ) to investigate their roles and their impact on downstream signaling cascades with RNA sequencing. Recombinant IFNa was used to induce an antiviral state before challenging cells with ISAV and IPNV. The knockouts significantly disrupt downstream antiviral signaling, with two knockouts, crfb1a and crfb5a , showing pronounced effects. During ISAV infection, the crfb1a KO group exhibited a marked reduction in the expression of critical signaling genes such as stat1b, stat2, stat6, and irf3 during ISAV infection, while irf7 was upregulated during IPNV infection. The crfb5a KO group exhibited reduced stat2 expression in ISAV infection and upregulated irf7 during IPNV infection. Despite these disruptions, ISGs such as Mx and isg15 maintained their expression levels across all knockout groups, suggesting potential alternative signaling pathways. Pathway analysis further revealed upregulation of cellular processes like actin regulation and phagosome activity, which may compensate for impaired immune signaling. These findings highlight the distinct roles of IFN receptor genes in mediating antiviral responses and underscore the complexity of IFN signaling in Atlantic salmon.

Background Spatial organization of the genome is fundamental for ensuring accurate gene expression. This process depends on the communication between gene promoters and distal cis -regulatory elements (CREs), which together make up 8% of the human genome and are supported by the chromatin structure. It is estimated that over 90% of disease-associated variants are located in the non-coding region of the genome and may affect CRE. For the cystic fibrosis transmembrane conductance regulator ( CFTR) gene, a complete understanding of tissue-specific CFTR expression and regulation is missing, in particular in the pancreas. Mechanistic insights into tissue-specific expression may provide clarity on the clinical heterogeneity observed in Cystic Fibrosis and CFTR-related disorders. Methods To understand the role of 3D chromatin architecture in establishing tissue-specific expression of the CFTR gene, we mapped chromatin interactions via circular chromosome conformation capture (4C) and epigenomic regulation through H3K27ac and DNase Hypersensitive site I (DHS) in Capan-1 pancreatic cells. Candidate regulatory regions are validated by luciferase reporter assay and CRISPR-knock out. Results We identified active regulatory regions not only around the CFTR gene but also outside the topologically associating domain (TAD). By performing functional assays, we validated our targets and revealed a cooperative effect of the −44 kb, −35 kb, +15.6 kb and 37.7 kb regions, which share common predicted transcription factor (TF) motifs. Comparative 3D genomic analysis and functional assays using the Caco-2 intestinal cell line revealed the presence of tissue-specific CREs. Conclusion By studying the chromatin architecture of the CFTR locus in Capan-1 cells, we demonstrated the involvement of multiple CREs upstream and downstream of the CFTR gene. We also extend our analysis to compare intestinal and pancreatic cells and provide information on the tissue-specificity of CRE. These findings highlight the importance of expanding the search for causative variants beyond the gene coding sequence but also by considering the tissue-specific 3D genome.

ABSTRACT Loss-of-function mutations in ADAMTSL4, a gene encoding an extracellular matrix-associated protein with incompletely understood biological roles, are linked to autosomal recessive disorders predominantly characterized by lens dislocation. Pupil ectopia, increased intraocular pressure, retinal detachment, cataracts, and skeletal abnormalities are also observed in some patients. To investigate ADAMTSL4 biology and related diseases we established a zebrafish knockout line using CRISPR/Cas9 genome editing. The generated zebrafish model harboured the c.234-351del mutation in adamstsl4 , reducing its mRNA levels by 75% in 6 days post fertilization (dpf) larvae, and predicting to produce an inactive protein (p.(Gln78Hisfs*127)). Forty percent of F3 knockout larvae (6 dpf) displayed lethal phenotypes characterized by multiple ocular and non-ocular developmental defects, including pericardial, perivitelline and periocular edema, absence of swim bladder, craniofacial malformations and microphthalmia. The remaining 60% larvae survived and displayed only reduced pupil area, indicating incomplete penetrance of the lethality. Histology revealed extracellular matrix (ECM) and intercellular junctions abnormalities within the cornea, iris, lens, and retinal pigment epithelium (RPE). Adult knockout zebrafish (6 months) presented phenotypes resembling ectopia lentis et pupillae and craniosynostosis, with optical defects in the lens and impaired visual function. ECM and cell junction disorganization in the cornea, lens and RPE were also present in these animals. Transcriptomic analysis revealed disrupted expression of genes involved in development, ECM and cell junctions among other biological processes. These findings show that a damtsl4 recapitulates key features of human ADAMTSL4 -related disorders and that this gene is essential for normal ECM structure, cell junctions and embryonic development. Highlights Zebrafish adamtsl4 knockout recapitulates human ADAMTSL4 -related phenotypes. adamtsl4 is involved in embryonic development. adamtsl4 participates in ECM organization and cell adhesion.

X-linked Lymphoproliferative Syndromes (XLP), which arise from mutations in the SH2D1A or XIAP genes, are characterized by the inability to control Epstein-Barr Virus (EBV) infection. While primary EBV infection triggers severe diseases in each, lymphomas occur at high rates with XLP-1 but not with XLP-2. Why XLP-2 patients are apparently protected from EBV-driven lymphomagenesis, in contrast to all other described congenital conditions that result in heightened susceptibility to EBV, remains a key open question. To gain insights, we cross-compared newly EBV infected versus immune stimulated B-cells from XLP-2 patients or upon XIAP CRISPR knockout, relative to healthy controls. XIAP perturbation impeded outgrowth of newly EBV-infected primary human B-cells, though had no impact on proliferation of B-cells stimulated by CD40 ligand and interleukin-21 or upon established EBV-immortalized lymphoblastoid cell lines (LCLs). B-cells from XLP-2 patients or in which XIAP was depleted by CRISPR editing exhibited a markedly lower EBV transformation efficiency than healthy control B-cells. Mechanistically, nascent EBV infection activated p53-mediated apoptosis signaling, whose effects on transforming B-cell death were counteracted by XIAP. In the absence of XIAP, EBV infection triggered high rates of apoptosis, not seen with CD40L/IL-21 stimulation. Moreover, inflammatory cytokines are present at high levels in XLP-2 patient serum with fulminant EBV infection, which heightened apoptosis induction in newly EBV-infected cells. These findings highlight the crucial role of XIAP in supporting early stages of EBV-driven B-cell immortalization and provide insights into the absence of EBV+ lymphoma in XLP-2 patients. Key points XIAP loss-of-function markedly impairs EBV+ B-cells outgrowth over the first week post-infection, particularly in the presence of IFN-γ. XIAP mutation impedes EBV-driven B-cell transformation by potentiating p53-driven caspase activation and apoptosis.