SpCas9-HF1 enhances accuracy of cell cycle-dependent genome editing by increasing HDR efficiency, and by reducing off-target effects and indel rates

In genome editing, it is important to avoid off-target mutations so as to reduce unexpected side effects, especially for therapeutic applications. Recently, several high-fidelity versions of SpCas9 have been developed to reduce off-target mutations. In addition to reducing off-target effects, highly efficient intended target gene correction is also essential to rescue protein functions that have been disrupted by single nucleotide polymorphisms. Homology-directed repair (HDR) corrects genes precisely using a DNA template. Our recent development of cell cycle-dependent genome editing has shown that regulation of Cas9 activation with an anti-CRISPR-Cdt1 fusion protein increases HDR efficiency and reduces off-target effects. In this study, to apply high-fidelity SpCas9 variants to cell cycle-dependent genome editing, we evaluated anti-CRISPR inhibition of high-fidelity SpCas9s. In addition, HDR efficiency of high-fidelity SpCas9s was addressed, identifying eSpCas9, SpCas9-HF1, and LZ3 Cas9 as promising candidates. Although eSpCas9 and LZ3 Cas9 showed decreased HDR efficiency in cell cycle-dependent genome editing, SpCas9-HF1 successfully achieved increased HDR efficiency and few off-target effects when co-expressed with an AcrIIA4-Cdt1 fusion.

YAP knockdown repressed autophagy in fibroblasts to accelerate wound healing through regulating En1/mTOR axis

OBJECTIVE

Wound repair dysfunction is becoming a major public health issue worldwide. Yes-associated protein (YAP) has previously been reported to be closely related to wound healing, while how YAP accelerates wound healing via regulating autophagy needs to be further probed.

MATERIALS AND METHODS

ICR male mice were involved in two independent animal experiments; the mice were randomly allocated into control, autophagy inhibitor (3-MA) (injection), and 3-MA (drip) group or control, si-NC, si-YAP group (8 mice for each). Full-thickness excisional wounds (8 mm) in mice were created by punch to construct an in vivo wound model to observe the effects of autophagy inhibitor (3-MA) (by injection and drip) and si-YAP by electrotransfection.

RESULTS

Firstly, we found that the autophagy inhibitor (3-MA) accelerated wound closure in vivo. Loss-of-function experiments subsequently revealed that YAP knockdown led to increased proliferation and migration of fibroblasts as well as reduced autophagy, resulting in accelerated wound healing. In addition, our results revealed that YAP could positively regulate Engrailed-1 (En1) expression in fibroblasts. En1 knockdown also promoted the proliferation and migration of fibroblasts, meanwhile resulting in increased mammalian target of rapamycin (mTOR) levels and reduced autophagy in fibroblasts.

CONCLUSIONS

YAP knockdown repressed autophagy in fibroblasts to accelerate wound closure by regulating the En1/mTOR axis.

Formation of the brain by stem cell divisions of large neuroblasts in Oikopleura dioica, a simple chordate

Stem cell division contributes to the generation of various cell types during animal development, especially a diverse pool of neural cells in the nervous system. One example is reiterated unequal stem cell divisions, in which a large stem cell undergoes a series of oriented unequal divisions to produce a chain of small daughter cells that differentiate. We show that reiterated unequal stem cell divisions are involved in the formation of the brain in simple chordate appendicularians (larvaceans). Two large neuroblasts in the anterior and middle of the brain-forming region of hatched larvae were observed. They produced at least 30 neural cells out of 96 total brain cells before completion of brain formation at 10 hours after fertilization by reiterated unequal stem cell divisions. The daughter cells of the anterior neuroblast were postmitotic, and the number was at least 19. The neuroblast produced small daughter neural cells posteriorly every 20 min. The neural cells first moved toward the dorsal side, turned in the anterior direction, aligned in a single line according to their birth order, and showed collective movement to accumulate in the anterior part of the brain. The anterior neuroblast originated from the right-anterior blastomeres of the eight-cell embryos and the right a222 blastomere of the 64-cell embryo. The posterior neuroblast also showed reiterated unequal stem cell divisions, and generated at least 11 neural cells. Sequential unequal stem cell divisions without stem cell growth have been observed in protostomes, such as insects and annelids. The results provide the first examples of this kind of stem cell division during brain formation in non-vertebrate deuterostomes.

The past, present, and future of artificial zinc finger proteins: design strategies and chemical and biological applications

Zinc finger proteins are abundant in the human proteome and are responsible for a variety of functions. The domains that constitute zinc finger proteins are compact spherical structures, each comprising approximately 30 amino acid residues, but they also have precise molecular factor functions: zinc binding and DNA recognition. Due to the biological importance of zinc finger proteins and their unique structural and functional properties, many artificial zinc finger proteins have been created and are expected to improve their functions and biological applications. In this study, we review previous studies on the redesign and application of artificial zinc finger proteins, focusing on the experimental results obtained by our research group. In addition, we systematically review various design strategies used to construct artificial zinc finger proteins and discuss in detail their potential biological applications, including gene editing. This review will provide relevant information to researchers involved or interested in the field of artificial zinc finger proteins as a potential new treatment for various diseases.

Cas9-Geminin and Cdt1-fused anti-CRISPR protein synergistically increase editing accuracy

Genome editing with CRISPR-Cas9, particularly for therapeutic purposes, should be accomplished via the homology-directed repair (HDR) pathway, which exhibits greater precision than other pathways. However, one of the issues to be solved is that genome editing efficiency with HDR is generally low. A Streptococcus pyogenes Cas9 (SpyCas9) fusion with human Geminin (Cas9-Gem) reportedly increases HDR efficiency slightly. In contrast, we found that regulation of SpyCas9 activity with an anti-CRISPR protein (AcrIIA4) fused to Chromatin licensing and DNA replication factor 1 (Cdt1) significantly increases HDR efficiency and reduces off-target effects. Here, another anti-CRISPR protein, AcrIIA5, was applied, and the combined use of Cas9-Gem and Anti-CRISPR+Cdt1 showed synergistic enhancement of HDR efficiency. The method may be applicable to various anti-CRISPR/CRISPR-Cas combinations.

An ImageJ-based tool for three-dimensional registration between different types of microscopic images

Three-dimensional (3D) registration (i.e., alignment) between two microscopic images is very helpful to study tissues that do not adhere to substrates, such as mouse embryos and organoids, which are often 3D rotated during imaging. However, there is no 3D registration tool easily accessible for experimental biologists. Here we developed an ImageJ-based tool which allows for 3D registration accompanied with both quantitative evaluation of the accuracy and reconstruction of 3D rotated images. In this tool, several landmarks are manually provided in two images to be aligned, and 3D rotation is computed so that the distances between the paired landmarks from the two images are minimized. By simultaneously providing multiple points (e.g., all nuclei in the regions of interest) other than the landmarks in the two images, the correspondence of each point between the two images, i.e., to which nucleus in one image a certain nucleus in another image corresponds, is quantitatively explored. Furthermore, 3D rotation is applied to one of the two images, resulting in reconstruction of 3D rotated images. We demonstrated that this tool successfully achieved 3D registration and reconstruction of images in mouse pre- and post-implantation embryos, where one image was obtained during live imaging and another image was obtained from fixed embryos after live imaging. This approach provides a versatile tool applicable for various tissues and species.

Importance of two-dimensional cation clusters induced by protein folding in intrinsic intracellular membrane permeability

Two-dimensional cation clusters formed on the surface of proteins play an important role in their intracellular translocation.

Repetitive short-pulsed illumination efficiently activates photoactivatable-Cre as continuous illumination in embryonic stem cells and pre-implantation embryos of transgenic mouse

The Cre-loxP system has been widely used for specific DNA recombination which induces gene inactivation or expression. Recently, photoactivatable-Cre (PA-Cre) proteins have been developed as a tool for spatiotemporal control of the enzymatic activity of Cre recombinase. Here, we generated transgenic mice bearing a PA-Cre gene and systematically investigated the conditions of photoactivation for the PA-Cre in embryonic stem cells (ESCs) derived from the transgenic mice and in a simple mathematical model. Cre-mediated DNA recombination was induced in 16% of the PA-Cre ESCs by 6 hr continuous illumination. We show that repetitive pulsed illumination efficiently induced DNA recombination with low light energy as efficient as continuous illumination in the ESCs (96 ± 15% of continuous illumination when pulse cycle was 2 s), which was also supported by a minimal mathematical model. DNA recombination by the PA-Cre was also successfully induced in the transgenic mouse pre-implantation embryos under the developed conditions. These results suggest that strategies based on repetitive pulsed illumination are efficient for the activation of photoactivatable Cre and, possibly other photo-switchable proteins.

Multicenter prospective trial of total gastrectomy versus proximal gastrectomy for upper third cT1 gastric cancer

BACKGROUND

The appropriate surgical procedure for patients with upper third early gastric cancer is controversial. We compared total gastrectomy (TG) with proximal gastrectomy (PG) in this patient population.

METHODS

A multicenter, non-randomized trial was conducted, with patients treated with PG or TG. We compared short- and long-term outcomes between these procedures.

RESULTS

Between 2009 and 2014, we enrolled 254 patients from 22 institutions; data from 252 were included in the analysis. These 252 patients were assigned to either the PG (n = 159) or TG (n = 93) group. Percentage of body weight loss (%BWL) at 1 year after surgery, i.e., the primary endpoint, in the PG group was significantly less than that of the TG group (- 12.8% versus - 16.9%; p = 0.0001). For short-term outcomes, operation time was significantly shorter for PG than TG (252 min versus 303 min; p < 0.0001), but there were no group-dependent differences in blood loss and postoperative complications. For long-term outcomes, incidence of reflux esophagitis in the PG group was significantly higher than that of the TG group (14.5% versus 5.4%; p = 0.02), while there were no differences in the incidence of anastomotic stenosis between the two (5.7% versus 5.4%; p = 0.92). Overall patient survival rates were similar between the two groups (3-year survival rates: 96% versus 92% in the PG and TG groups, respectively; p = 0.49).

CONCLUSIONS

Patients who underwent PG were better able to control weight loss without worsening the prognosis, relative to those in the TG group. Optimization of a reconstruction method to reduce reflux in PG patients will be important.

Nintedanib in patients with progressive fibrosing interstitial lung diseases-subgroup analyses by interstitial lung disease diagnosis in the INBUILD trial: a randomised, double-blind, placebo-controlled, parallel-group trial

BACKGROUND

The INBUILD trial investigated the efficacy and safety of nintedanib versus placebo in patients with progressive fibrosing interstitial lung diseases (ILDs) other than idiopathic pulmonary fibrosis (IPF). We aimed to establish the effects of nintedanib in subgroups based on ILD diagnosis.

METHODS

The INBUILD trial was a randomised, double-blind, placebo-controlled, parallel group trial done at 153 sites in 15 countries. Participants had an investigator-diagnosed fibrosing ILD other than IPF, with chest imaging features of fibrosis of more than 10% extent on high resolution CT (HRCT), forced vital capacity (FVC) of 45% or more predicted, and diffusing capacity of the lung for carbon monoxide (DLco) of at least 30% and less than 80% predicted. Participants fulfilled protocol-defined criteria for ILD progression in the 24 months before screening, despite management considered appropriate in clinical practice for the individual ILD. Participants were randomly assigned 1:1 by means of a pseudo-random number generator to receive nintedanib 150 mg twice daily or placebo for at least 52 weeks. Participants, investigators, and other personnel involved in the trial and analysis were masked to treatment assignment until after database lock. In this subgroup analysis, we assessed the rate of decline in FVC (mL/year) over 52 weeks in patients who received at least one dose of nintedanib or placebo in five prespecified subgroups based on the ILD diagnoses documented by the investigators: hypersensitivity pneumonitis, autoimmune ILDs, idiopathic non-specific interstitial pneumonia, unclassifiable idiopathic interstitial pneumonia, and other ILDs. The trial has been completed and is registered with ClinicalTrials.gov, number NCT02999178.

FINDINGS

Participants were recruited between Feb 23, 2017, and April 27, 2018. Of 663 participants who received at least one dose of nintedanib or placebo, 173 (26%) had chronic hypersensitivity pneumonitis, 170 (26%) an autoimmune ILD, 125 (19%) idiopathic non-specific interstitial pneumonia, 114 (17%) unclassifiable idiopathic interstitial pneumonia, and 81 (12%) other ILDs. The effect of nintedanib versus placebo on reducing the rate of FVC decline (mL/year) was consistent across the five subgroups by ILD diagnosis in the overall population (hypersensitivity pneumonitis 73·1 [95% CI -8·6 to 154·8]; autoimmune ILDs 104·0 [21·1 to 186·9]; idiopathic non-specific interstitial pneumonia 141·6 [46·0 to 237·2]; unclassifiable idiopathic interstitial pneumonia 68·3 [-31·4 to 168·1]; and other ILDs 197·1 [77·6 to 316·7]; p=0·41 for treatment by subgroup by time interaction). Adverse events reported in the subgroups were consistent with those reported in the overall population.

INTERPRETATION

The INBUILD trial was not designed or powered to provide evidence for a benefit of nintedanib in specific diagnostic subgroups. However, its results suggest that nintedanib reduces the rate of ILD progression, as measured by FVC decline, in patients who have a chronic fibrosing ILD and progressive phenotype, irrespective of the underlying ILD diagnosis.

FUNDING

Boehringer Ingelheim.

CNS distribution, signalling properties and central effects of G-protein coupled receptor 4

Information on the distribution and biology of the G-protein coupled receptor 4 (GPR4) in the brain is limited. It is currently thought that GPR4 couples to Gs proteins and may mediate central respiratory sensitivity to CO2. Using a knock-in mouse model, abundant GPR4 expression was detected in the cerebrovascular endothelium and neurones of dorsal raphe, retro-trapezoidal nucleus locus coeruleus and lateral septum. A similar distribution was confirmed using RNAscope in situ hybridisation. In HEK293 cells, overexpressing GPR4, it was highly constitutively active at neutral pH with little further increase in cAMP towards acidic pH. The GPR4 antagonist NE 52-QQ57 effectively blocked GPR4-mediated cAMP accumulation (IC50 26.8 nM in HEK293 cells). In HUVEC which natively express GPR4, physiological acidification (pH 7.4-7.0) resulted in a cAMP increase by ∼55% which was completely prevented by 1 μM NE 52-QQ57. The main extracellular organic acid, l-lactic acid (LL; 1-10 mM), suppressed pH dependent activation of GPR4 in HEK293 and HUVEC cells, suggesting allosteric negative modulation. In unanaesthetised mice and rats, NE 52-QQ57 (20 mg kg-1) reduced ventilatory response to 5 and 10% CO2. In anaesthetised rats, systemic administration of NE 52-QQ57 (up to 20 mg kg-1) had no effect on hemodynamics, cerebral blood flow and blood oxygen level dependent responses. Central administration of NE 52-QQ57 (1 mM) in vagotomised anaesthetised rats did not affect CO2-induced respiratory responses. Our results indicate that GPR4 is expressed by multiple neuronal populations and endothelium and that its pH sensitivity is affected by level of expression and LL. NE 52-QQ57 blunts hypercapnic response to CO2 but this effect is absent under anaesthesia, possibly due to the inhibitory effect of LL on GPR4.

Dacron-Covered Stent Therapy for Portal Vein Tumor Thrombus in Hepatocellular Carcinoma

A tumor thrombus of the portal vein is refractory to therapy and constitutes a serious prognostic factor in hepatocellular carcinoma. For the purpose of treating portal vein tumor thrombus by restoring the blood flow and preventing recurrent ingrowth of tumor, we devised a metallic stent partially covered with a Dacron mesh sheet, and a coaxial percutaneous delivery system. One half of the wall of a Gianturco Z-stent was covered with a sheet of 0.25-mm-thick Dacron mesh, fixed to the stent wall with nylon threads. The covered stent was implanted in a patient with severe main portal vein stenosis due to tumor thrombus protruding from the left portal vein branch. Immediately after stent placement the tumor stenosis was effectively dilated, the portal blood flow restored, and the portal hypertension relieved. CT and angiography after 8 months still showed complete portal vein patency. Intrahepatic tumor dissemination or other complications were not observed. Intraportal placement of a covered metallic stent appears to be an efficacious therapy of major portal tumor thrombi.

Investigating the pressure-reducing effect of wound dressings

OBJECTIVE

Currently, polyurethane foam dressings are commercially available from many manufacturers. However, the pressure-reducing effect is expected to differ by the formulation and combination of the main and secondary ingredients and by manufacturing method. In this study, we investigated the effects of pressure reduction using dressing materials with various structural characteristics, including polyurethane foam dressings based on the engineering point of view, focusing on the dry state.

METHOD

Pressure was measured in a model that simulated compression on the sacral region in a decubitus position. Pressure was measured for different dressings: ten products, consisting of five types of material (polyurethane foam, hydropolymeric, Hydrofiber, hydrocolloid, and low-adherent absorbent).

RESULTS

All dressings used in this study showed significantly reduced pressure. ALLEVYN Non-Adhesive had the lowest pressure at 35.833 ± 1.155 mmHg, and DuoDERM Extra Thin CGF had the highest pressure at 66.867 ± 1.060 mmHg. The pressure of the control was 74.667 ± 1.405 mmHg. The other dressings were: ALLEVYN Adhesive: 44.233 ± 0.777 mmHg; ALLEVYN Gentle Border: 46.967 ± 1.537mmHg; Mepilex Border: 53.867 ± 0.231 mmHg; Biatain Silicone: 56.000 ± 0.520 mmHg; TIELLE: 57.267 ± 3.403 mmHg;Versiva XC: 65.900 ± 0.800 mmHg; DuoDERM CGF: 57.267 ± 1.007 mmHg; and Melolin: 53.433 ± 1.973 mmHg.

CONCLUSION

The pressure-reducing effect of dressing differs not only by material type but also by product. That is, the pressure-reducing effect can differ even if the dressings are of the same material type, such as polyurethane foam. Our study investigated only the effect of materials and structural characteristics on the cushion of dressings in the dry state. Therefore, further investigation is needed to confirm the effect of pressure reduction by dressing to meet the conditions in the clinic.

Inferolateral marginal orbitectomy: a simple adjuvant technique for orbital decompression

The number of patients with mild exophthalmos, without severe eye symptoms, who wish to undergo aesthetic orbital decompression, is increasing. Removal of the lateral and inferior orbital walls is a common procedure for mild to moderate exophthalmos. However, the limited space between the globe and the orbital wall is often troublesome for surgeons introducing surgical devices. As a result, the decompression tends to be insufficient in the posterior region of the orbit. We describe a simple adjuvant surgical technique to address this limitation. Through a laterally extended, transconjunctival approach, the inferior and lateral margins of the orbit are removed in a crescent shape before the actual decompression. This manoeuvre widens the working space and offers better visibility, enabling sufficient removal of the orbital walls. The technique presented facilitates the approach to the posterior regions of the orbit, enabling surgeons to more easily perform orbital decompression.

Dose-saving isolation procedure in percutaneous ethanol sclerotherapy for venous malformations

OBJECTIVES

To evaluate the feasibility and effectiveness of an isolation technique during ethanol injection sclerotherapy for venous malformations (VMs) in the head and neck region.

METHODS

The subjects were 23 patients with 35 VM lesions in the head and neck, treated between 1999 and 2012. The mean lesion area was 3.75 ± 3.09 cm(2) (±standard deviation). We confirmed the contour of the lesions to be treated on a fully filled image on direct injection cisternography, and observed patterns of communicating drainage to systemic veins. The cisterns were evacuated by squeezing and were isolated by manual compression of the communicators. Ethanol (94.5%) with a contrast agent was then injected into both isolable and unisolable lesions, up to a total volume of 1 mL/cm(2), avoiding complications. We investigated the relationship between lesion size and injected ethanol dose, and also dose per unit area.

RESULTS

Both manual evacuation by compression and isolation were performed in 20 (57.1%) isolable lesions, but not in 15 unisolable lesions. The mean injected ethanol dose was 0.65 ± 0.31 mL/cm(2) overall, 0.70 ± 0.32 in isolable and 0.59 ± 0.30 in unisolable lesions (NS). However, the injected ethanol dose was significantly lower for lesions sized >6 cm. Complete to near-complete shrinkage was observed in all isolable lesions, and in 60% of unisolable lesions (P < 0.05). Clinical outcome seemed unrelated to the injected ethanol dose or the dose per unit area. There was one case of recurrence and one complication in the unisolable lesions. No further relapses or complications were observed during the follow-up period of 38.6 ± 12.3 months.

CONCLUSIONS

Clinical outcome was related to the isolability not to the injected dose. The isolation appears useful for improving the safety and effectiveness of ethanol sclerotherapy for VM.

Potential pitfalls in volume reduction for the treatment of Proteus syndrome

Proteus syndrome is a rare congenital hamartomatous condition that is characterised by a wide range of malformations. Skin and skeletal developmental malformations are common and may manifest as significant physical anomalies. However, few reports have discussed surgical treatment. A 37-year-old woman presented with disproportionate enlargement of the right buttock, which required volume reduction. The overgrown tissue was combined with vascular malformations, which in our patient were extremely thick. The patient experienced massive blood loss during the procedure, due to which a blood transfusion was performed. Pathological findings revealed partial lipohyperplasia with venous malformations. Thus, during operations including incomplete excision, massive bleeding is always a possibility, but is not commonly described in these instances.

Inhibitory effect of statins on inflammatory cytokine production from human bronchial epithelial cells

Statins are 3-hydroxy-3-methylglutaryl-co-enzyme A reductase inhibitors of cholesterol biosynthesis, and have been reported to exert pleiotropic effects on cellular signalling and cellular functions involved in inflammation. Recent reports have demonstrated that previous statin therapy reduced the risk of pneumonia or increased survival in patients with community-acquired pneumonia. However, the precise mechanisms responsible for these effects are unclear. In the present study, we examined the effects of statins on cytokine production from lipopolysaccharide (LPS)-stimulated human bronchial epithelial cells (BEAS-2B). Interleukin (IL)-6 and IL-8 mRNA expression and protein secretion in LPS-stimulated cells were inhibited significantly by the lipophilic statin pitavastatin and the hydrophilic statin pravastatin. As these inhibitory effects of statin were negated by adding mevalonate, the anti-inflammatory effects of statins appear to be exerted via the mevalonic cascade. In addition, the activation levels of Ras homologue gene family A (RhoA) in BEAS-2B cells cultured with pitavastatin were significantly lower than those without the statin. These results suggest that statins have anti-inflammatory effects by reducing cytokine production through inhibition of the mevalonic cascade followed by RhoA activation in the lung.

Prevention of gastroduodenal content reflux and delayed gastric emptying after esophagectomy: gastric tube reconstruction with duodenal diversion plus Roux-en-Y anastomosis

Reflux of gastroduodenal contents and delayed gastric emptying are the most common and serious problems after esophagectomy with gastric reconstruction. However, attempts to reduce the above symptoms, surgically as well as non-surgically, had no or limited effect. To address this issue, we performed retrosternal gastric reconstruction with duodenal diversion plus Roux-en-Y anastomosis (RY) in eight patients with thoracic esophageal cancer and compared the outcomes with control patients who underwent standard reconstruction. The procedure is simple, safe, and not associated with any postoperative complications. The pancreatic amylase concentrations in the gastric juice samples on postoperative day 2 were slightly lower in the non-RY group than in the RY group (1884 ± 2152 vs. 25,790 ± 23,542IU/mL, respectively, P= 0.07). Postoperative endoscopic examination showed neither reflux esophagitis nor residual gastric content in the RY group. Quality of life assessed by the Dysfunction After Upper Gastrointestinal Surgery-32 questionnaire postoperatively was significantly better in the RY group than in the non-RY group for 'decreased physical activity,''symptoms of reflux,''nausea and vomiting,' and 'pain.' The results of this pilot study suggest that gastric reconstruction with duodenal diversion plus RY seems effective in improving both the reflux and delayed gastric emptying. The benefits of this procedure need to be further assessed in a large-scale, randomized controlled trial.