Engineering of Zinc Finger Nucleases Through Structural Modeling Improves Genome Editing Efficiency in Cells.

Genome Editing is widely used in biomedical research and medicine. Zinc finger nucleases (ZFNs) are smaller in size than transcription activator-like effector (TALE) nucleases (TALENs) and CRISPR-Cas9. Therefore, ZFN-encoding DNAs can be easily packaged into a viral vector with limited cargo space, such as adeno-associated virus (AAV) vectors, for in vivo and clinical applications. ZFNs have great potential for translational research and clinical use. However, constructing functional ZFNs and improving their genome editing efficiency is extremely difficult. Here, the efficient construction of functional ZFNs and the improvement of their genome editing efficiency using AlphaFold, Coot, and Rosetta are described. Plasmids encoding ZFNs consisting of six fingers using publicly available zinc-finger resources are assembled. Two functional ZFNs from the ten ZFNs tested are successfully obtained. Furthermore, the engineering of ZFNs using AlphaFold, Coot, or Rosetta increases the efficiency of genome editing by 5%, demonstrating the effectiveness of engineering ZFNs based on structural modeling.

Water Condensation in the Nanoscale Pores of Pt/C Catalyst Particles and Its Impact on Catalyst Utilization: A Simulation Based on a Reconstructed Structure from Nanoimaging.

In polymer electrolyte membrane fuel cells, carbon-supported platinum (Pt/C) catalyst particles require sufficient water condensation within the nanoscale pores to effectively utilize the interior Pt catalysts. Since experimental visualizations with nanoscale precision of this phenomenon are not yet possible, we utilized a Pt/C catalyst particle reconstructed from segmented nanoimaging of a catalyst powder, which served as the computational domain for lattice density functional theory (LDFT) simulation of water condensation. Paired with experimental water uptake data, LDFT successfully simulated high-resolution water condensation, capturing both thin-film and capillary water condensation phenomena. Using a simple proton movement method within the water network, we reproduced the Pt utilization data from a CO stripping experiment. Our findings highlight that at low relative humidity (RH), Pt utilization is influenced by thin water film formations, mainly dictated by the wettability properties of surfaces within primary pores and the Pt/C catalyst particle's exterior. Conversely, at high RH, Pt utilization is attributed to capillary water condensation in medium-to-large sized pores. This approach contributes a qualitative and quantitative discussion on hypotheses regarding the mechanism of Pt utilization, supporting recent studies (e.g., Girod, R.; Nat. Catal. 2023, 6, (5), 383-391).

A more efficient method for generating glioblastoma-multiforme model in mice using genome editing technology.

The elucidation of the properties of malignant glioma and development of therapeutic methods require glioblastoma-multiforme mice model with characteristics such as invasiveness, multinuclearity, and ability for mitosis. A previous study has shown that overexpression of active HRas (HRasL61) in neural stem/progenitor cells (NSCs) isolated from p53 knockout (KO) mice could induce glioma-initiating cells (GICs). The orthotopically transplantation of 10 cells into the forebrain of immunodeficient mice resulted in the development of glioblastoma multiforme-like malignant brain tumors. In this study, we successfully induced GICs from wild-type fetal NSCs. Using CRISPR/Cas9, we obtained p53 KO NSCs. HRasL61 was additionally overexpressed in p53 KO NSCs. p53-/HRasL61+ cells were cloned and then transplanted into immunodeficient mice. p53-/HRasL61+ cells formed glioblastoma multiforme-like tumors. Further, GIC markers were strongly expressed in p53-/HRasL61+ cells. Therefore, p53-/HRasL61+ cell is an induced GIC. A CRISPR/Cas9-based method for inducing GIC is much more efficient than a KO mice-based method. This study provides a promising framework for easily creating glioblastoma model in mice.

Targeting c-Jun Is a Potential Therapy for Luminal Breast Cancer Bone Metastasis.

Luminal breast cancer has the highest bone metastasis frequency among all breast cancer subtypes; however, its metastatic mechanism has not been elucidated because of a lack of appropriate models. We have previously developed useful bone metastatic cell lines of luminal breast cancer using MCF7 cells. In this study, we characterized bone metastatic MCF7-BM cell lines and identified c-Jun as a novel bone metastasis marker of luminal breast cancer. The protein level of c-Jun was upregulated in MCF7-BM cells compared with that in parental cells, and its deficiency resulted in the suppression of tumor cell migration, transformation, and reduced osteolytic ability. In vivo, dominant-negative c-Jun exhibited smaller bone metastatic lesions and a lower metastatic frequency. Histologic analysis revealed that c-Jun expression was heterogeneous in bone metastatic lesions, whereas c-Jun overexpression mediated a vicious cycle between MCF7-BM cells and osteoclasts by enhancing calcium-induced migration and releasing the osteoclast activator BMP5. Pharmacological inhibition of c-Jun by the Jun amino-terminal kinase (JNK) inhibitor JNK-IN-8 effectively suppressed tumorigenesis and bone metastasis in MCF7-BM cells. Furthermore, c-Jun downstream signals were specifically correlated with the clinical prognosis of patients with the luminal subtype of breast cancer. Our results illustrate the potential benefits of a therapy that targets c-Jun to prevent bone metastasis in luminal breast cancer. IMPLICATIONS: c-Jun expression mediates bone metastasis in luminal breast cancer by forming a vicious cycle in the bone microenvironment, which reveals potential strategies for subtype-specific bone metastasis therapy.

HOXB7 induces STAT3-mediated transformation and lung metastasis in immortalized mammary gland NMuMG cells.

The homeobox family genes are often dysregulated in various cancer types. Particularly HOXB7 amplification and overexpression correlate with poor prognosis in various cancer such as gastric, pancreatic, and lung cancers. Moreover, HOXB7 is known to contribute to cancer progression by promoting epithelial to mesenchymal transition, anticancer drug resistance, and angiogenesis. In this study, we show that HOXB7 is coamplified with ERBB2 in a subset of breast cancer patients and HOXB7 expression correlates with poor prognosis in HER2-positive breast cancer patients. This clinical observation is supported by the following results-HOXB7 overexpression in an immortalized murine mammary gland epithelial cell line NMuMG induces cellular transformation in vitro, tumorigenesis, and lung metastasis through the activation of JAK-STAT signaling.

Immobilization of a Broad Range of Polypeptides on the Frustule of the Diatom Thalassiosira pseudonana.

Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. One recently developed technique, living diatom silica immobilization (LiDSI), has made it possible to immobilize proteins, including multimeric and redox enzymes, via a cellular excretion system onto the silica frustule of the marine diatom Thalassiosira pseudonana. However, the number of application examples so far is limited, and the type of proteins appropriate for the technique is still enigmatic. Here, we applied LiDSI to six industrially relevant polypeptides, including protamine, metallothionein, phosphotriesterase, choline oxidase, laccase, and polyamine synthase. Protamine and metallothionein were successfully immobilized on the frustule as protein fusions with green fluorescent protein (GFP) at the N terminus, indicating that LiDSI can be used for polypeptides which are rich in arginine and cysteine. In contrast, we obtained mutants for the latter four enzymes in forms without green fluorescent protein. Immobilized phosphotriesterase, choline oxidase, and laccase showed enzyme activities even after the purification of frustule in the presence of 1% (wt/vol) octylphenoxy poly(ethyleneoxy)ethanol. An immobilized branched-chain polyamine synthase changed the intracellular polyamine composition and silica nanomorphology. These results illustrate the possibility of LiDSI for industrial applications. IMPORTANCE Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. Living diatom silica immobilization (LiDSI) is a recently developed technique for in vivo protein immobilization on the diatom frustule. We aimed to explore the possibility of using LiDSI for industrial applications by successfully immobilizing six polypeptides: (i) protamine (Oncorhynchus keta), a stable antibacterial agent; (ii) metallothionein (Saccharomyces cerevisiae), a metal adsorption molecule useful for bioremediation; (iii) phosphotriesterase (Sulfolobus solfataricus), a scavenger for toxic organic phosphates; (iv) choline oxidase (Arthrobacter globiformis), an enhancer for photosynthetic activity and yield of plants; (v) laccase (Bacillus subtilis), a phenol oxidase utilized for delignification of lignocellulosic materials; and (vi) branched-chain polyamine synthase (Thermococcus kodakarensis), which produces branched-chain polyamines important for DNA and RNA stabilization at high temperatures. This study provides new insights into the field of applied biological materials.

Editing of DNA methylation using CRISPR/Cas9 and a ssDNA template in human cells.

Programmable DNA methylation is required for understanding of transcriptional regulation and elucidating gene functions. We previously reported that MMEJ-based promoter replacement enabled targeted DNA methylation in human cells. ssDNA-mediated knock-in has recently been reported to completely reduce random integrations. We speculated that by changing MMEJ-to ssDNA-based knock-in, targeted DNA methylation may be achieved through a hemimethylation-symmetric methylation pathway. We herein successfully developed a new system that enables the replacement of an unmethylated promoter with a methylated ssDNA promoter through ssDNA-based knock-in. A DNA methylation ratio of approximately 100% was achieved at the cancer-associated gene SP3 in HEK293 cells. The present results provide a promising framework for artificial epigenetic modifications.

Isolation and characterization of cancer stem cells derived from human glioblastoma.

Cancer stem cell (CSC) is considered as a cause of cancer recurrence and metastasis. Simultaneously CSCs are responsible for the heterogeneous population in tumor tissues due to their differentiation potential. However, the characterizations of CSCs are still not enough and cancer stem cell lines widely available is desired to be established for the advancement of cancer research. In this study, we tried to isolate and characterize stem like cells from human glioblastoma cell line U-251MG cells. U-251MG P1 cells, which was previously condensed in the presence of hyaluronic acid as CD44 positive population were subjected to single cell isolation procedure. Although 5 clones were isolated, only one clone exhibited high expression of CD44, Nanog, OCT3/4 and SOX2, and named U-251MGSC1. The sphere forming ability of U-251MGSC1 cell was significantly higher than the parental U-251MG cells. Tumorigenicity of U-251MG-SC1 cells were higher than that of U-251MG cells. U-251MGSC1 cells exhibited higher expression of CD44, SOX2, Nestin and A2B5 than U-251MG cells in vitro and in vivo. The expression of GFAP and NF-M was enhanced when the cells were treated with the conditioned medium of U-251MG cells indicating the potential of differentiation. Sphere forming ability was more efficient than that of U-251MG cells and was enhanced in the presence of hyaluronic acid, which enhanced the cell growth as well. U-251MGSC1 cells exhibited rapid growth tumor in nude mice and efficient metastatic ability in transmembrane assay when compared with U-251MG cells. As the result, we concluded U-251MGSC1 cell was a glioblastoma CSC line derived from the parental U-251MG cells. U-251MGSC1 cells will be a good tool to develop effective therapeutic agents against CSCs and to elucidate the properties of glioma derived CSCs and the mechanism of tumor development in brain.

A CRISPR/Cas9-based method for targeted DNA methylation enables cancer initiation in B lymphocytes.

Targeted DNA methylation is important for understanding transcriptional modulation and epigenetic diseases. Although CRISPR-Cas9 has potential for this purpose, it has not yet been successfully used to efficiently introduce DNA methylation and induce epigenetic diseases. We herein developed a new system that enables the replacement of an unmethylated promoter with a methylated promoter through microhomology-mediated end joining-based knock-in. We successfully introduced an approximately 100% DNA methylation ratio at the cancer-associated gene SP3 in HEK293 cells. Moreover, engineered SP3 promoter hypermethylation led to transcriptional suppression in human B lymphocytes and induced B-cell lymphoma. Our system provides a promising framework for targeted DNA methylation and cancer initiation through epimutations.

Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice.

Supplementing wildtype copies of functionally defective genes with adeno-associated virus (AAV) is a strategy being explored clinically for various retinal dystrophies. However, the low cargo limit of this vector allows its use in only a fraction of patients with mutations in relatively small pathogenic genes. To overcome this issue, we developed a single AAV platform that allows local replacement of a mutated sequence with its wildtype counterpart, based on combined CRISPR-Cas9 and micro-homology-mediated end-joining (MMEJ). In blind mice, the mutation replacement rescued approximately 10% of photoreceptors, resulting in an improvement in light sensitivity and an increase in visual acuity. These effects were comparable to restoration mediated by gene supplementation, which targets a greater number of photoreceptors. This strategy may be applied for the treatment of inherited disorders caused by mutations in larger genes, for which conventional gene supplementation therapy is not currently feasible.

In vivo and in vitro knockout system labelled using fluorescent protein via microhomology-mediated end joining.

Gene knockout is important for understanding gene function and genetic disorders. The CRISPR/Cas9 system has great potential to achieve this purpose. However, we cannot distinguish visually whether a gene is knocked out and in how many cells it is knocked out among a population of cells. Here, we developed a new system that enables the labelling of knockout cells with fluorescent protein through microhomology-mediated end joining-based knock-in. Using a combination with recombinant adeno-associated virus, we delivered our system into the retina, where the expression of Staphylococcus aureus Cas9 was driven by a retina ganglion cell (RGC)-specific promoter, and knocked out carnitine acetyltransferase (CAT). We evaluated RGCs and revealed that CAT is required for RGC survival. Furthermore, we applied our system to Keap1 and confirmed that Keap1 is not expressed in fluorescently labelled cells. Our system provides a promising framework for cell type-specific genome editing and fluorescent labelling of gene knockout based on knock-in.

Ecel1 Knockdown With an AAV2-Mediated CRISPR/Cas9 System Promotes Optic Nerve Damage-Induced RGC Death in the Mouse Retina.

Purpose: To assess the therapeutic potential of endothelin-converting enzyme-like 1 (Ecel1) in a mouse model of optic nerve crush. Methods: Ecel1 expression was evaluated with real time quantitative (qRT)-PCR, Western blotting, and immunohistochemistry in mouse retinas after optic nerve crush. Vinblastine administration to the optic nerve and the intravitreal injection of N-methyl-d-aspartate (NMDA) were used to assess Ecel1 gene expression. Ecel1 was deleted with an adeno-associated viral (AAV) clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas9 system, and retinal ganglion cell (RGC) survival was investigated with retrograde labeling, qRT-PCR, and visual evoked potential. Results: Optic nerve crush induced Ecel1 expression specifically in the RGCs, peaking on day 4 after optic nerve crush. Ecel1 gene expression was induced by the vinblastine-induced inhibition of axonal flow, but not by NMDA-induced excitotoxicity, even though both are triggers of RGC death. Knockdown of Ecel1 promoted the loss of RGCs after optic nerve crush. Conclusions: Our data suggest that Ecel1 induction is part of the retinal neuroprotective response to axonal injury in mice. These findings might provide insight into novel therapeutic targets for the attenuation of RGC damage, such as occurs in traumatic optic neuropathy.

Discovery of a Novel Sn(II)-Based Oxide ß-SnMoO4 for Daylight-Driven Photocatalysis.

Daylight-driven photocatalysts have attracted much attention in the context of "green" technology. Although various active materials have been reported and their applications are rapidly increasing, many are discovered after enormous experimental efforts. Herein the discovery of a novel oxide photocatalyst, ß-SnMoO4, is demonstrated via a rational search of 3483 known and hypothetical compounds with various compositions and structures over the whole range of SnO-MO q/2 (M: Ti, Zr, and Hf (q = 4); V, Nb, and Ta (q = 5); Cr, Mo, and W (q = 6)) pseudobinary systems. Screening using thermodynamic stability, band gap, and band-edge positions by density functional theory calculations identifies ß-SnMoO4 as a potential target. Then a low temperature route is used to successfully synthesize the novel crystal, which is confirmed by X-ray powder diffraction and Mössbauer spectroscopy. ß-SnMoO4 is active for the photocatalytic decomposition of a methylene blue solution under daylight and its activity is comparable to a known photocatalyst, ß-SnWO4.

MicroRNA-302 switch to identify and eliminate undifferentiated human pluripotent stem cells.

The efficiency of pluripotent stem cell differentiation is highly variable, often resulting in heterogeneous populations that contain undifferentiated cells. Here we developed a sensitive, target-specific, and general method for removing undesired cells before transplantation. MicroRNA-302a-5p (miR-302a) is highly and specifically expressed in human pluripotent stem cells and gradually decreases to basal levels during differentiation. We synthesized a new RNA tool, miR-switch, as a live-cell reporter mRNA for miR-302a activity that can specifically detect human induced pluripotent stem cells (hiPSCs) down to a spiked level of 0.05% of hiPSCs in a heterogeneous population and can prevent teratoma formation in an in vivo tumorigenicity assay. Automated and selective hiPSC-elimination was achieved by controlling puromycin resistance using the miR-302a switch. Our system uniquely provides sensitive detection of pluripotent stem cells and partially differentiated cells. In addition to its ability to eliminate undifferentiated cells, miR-302a switch also holds great potential in investigating the dynamics of differentiation and/or reprograming of live-cells based on intracellular information.

Optoelectronic properties of valence-state-controlled amorphous niobium oxide.

In order to understand the optoelectronic properties of amorphous niobium oxide (a-NbO x ), we have investigated the valence states, local structures, electrical resistivity, and optical absorption of a-NbO x thin films with various oxygen contents. It was found that the valence states of Nb ion in a-NbO x films can be controlled from 5+ to 4+ by reducing oxygen pressure during film deposition at room temperature, together with changing the oxide-ion arrangement around Nb ion from Nb2O5-like to NbO2-like local structure. As a result, a four orders of magnitude reduction in the electrical resistivity of a-NbO x films was observed with decreasing oxygen content, due to the carrier generation caused by the appearance and increase of an oxygen-vacancy-related subgap state working as an electron donor. The tunable optoelectronic properties of a-NbO x films by valence-state-control with oxygen-vacancy formation will be useful for potential flexible optoelectronic device applications.

A Powerful CRISPR/Cas9-Based Method for Targeted Transcriptional Activation.

Targeted transcriptional activation of endogenous genes is important for understanding physiological transcriptional networks, synthesizing genetic circuits, and inducing cellular phenotype changes. The CRISPR/Cas9 system has great potential to achieve this purpose, however, it has not yet been successfully used to efficiently activate endogenous genes and induce changes in cellular phenotype. A powerful method for transcriptional activation by using CRISPR/Cas9 was developed. Replacement of a methylated promoter with an unmethylated one by CRISPR/Cas9 was sufficient to activate the expression of the neural cell gene OLIG2 and the embryonic stem cell gene NANOG in HEK293T cells. Moreover, CRISPR/Cas9-based OLIG2 activation induced the embryonic carcinoma cell line NTERA-2 to express the neuronal marker ßIII-tubulin.

Loss of ADAR1 in human iPS cells promotes caspase3-mediated apoptotic cell death.

Adenosine deaminases acting on RNA (ADARs) convert adenosine residues to inosine specifically in double-stranded RNAs. In this study, we investigated the function of primary RNA editing enzyme ADAR1 in pluripotent stem cells and found that loss of ADAR1 in human iPS cells promotes caspase3-mediated cell death. However, ADAR1 knockdown (KD) did not alter cell morphology, alkaline phosphatase (AP) staining activities and the expression levels of pluripotent marker genes, indicating that ADAR1 is dispensable for maintenance of pluripotency. Furthermore, ADAR1-KD iPS cells did not change proliferation rate. These findings extended the role of ADAR1 and might open the road for understanding pluripotent state more deeply.

Efficient Detection and Purification of Cell Populations Using Synthetic MicroRNA Switches.

Isolation of specific cell types, including pluripotent stem cell (PSC)-derived populations, is frequently accomplished using cell surface antigens expressed by the cells of interest. However, specific antigens for many cell types have not been identified, making their isolation difficult. Here, we describe an efficient method for purifying cells based on endogenous miRNA activity. We designed synthetic mRNAs encoding a fluorescent protein tagged with sequences targeted by miRNAs expressed by the cells of interest. These miRNA switches control their translation levels by sensing miRNA activities. Several miRNA switches (miR-1-, miR-208a-, and miR-499a-5p-switches) efficiently purified cardiomyocytes differentiated from human PSCs, and switches encoding the apoptosis inducer Bim enriched for cardiomyocytes without cell sorting. This approach is generally applicable, as miR-126-, miR-122-5p-, and miR-375-switches purified endothelial cells, hepatocytes, and insulin-producing cells differentiated from hPSCs, respectively. Thus, miRNA switches can purify cell populations for which other isolation strategies are unavailable.

Localisation of bovine colostral odorant-binding protein (bcOBP) mRNAs in several tissues of bovine body.

Bovine colostral odorant-binding protein (bcOBP) is a novel protein found in bovine colostrum and belonging to the lipocalin superfamily. Most of them are secretory proteins. We have examined the localisation of bcOBP messenger RNA in several tissues. The expression of bcOBP messenger RNAs was followed in bovine principal organs and female reproductive tracts with in situ hybridisation, but the localisation of it was not detected. The expression levels of bcOBP mRNAs were also extremely low in those tissues. On the other hand, the expression of bcOBP messenger RNAs has not been found in the airway epithelia and the gallbladder. These results suggest that bcOBP messenger RNAs are expressed in bovine several tissues without its localisation. In conclusion, the localisation of bcOBP messenger RNAs in bovine several tissues was not found.