Engineering APOBEC3A deaminase for highly accurate and efficient base editing.

Cytosine base editors (CBEs) are effective tools for introducing C-to-T base conversions, but their clinical applications are limited by off-target and bystander effects. Through structure-guided engineering of human APOBEC3A (A3A) deaminase, we developed highly accurate A3A-CBE (haA3A-CBE) variants that efficiently generate C-to-T conversion with a narrow editing window and near-background level of DNA and RNA off-target activity, irrespective of methylation status and sequence context. The engineered deaminase domains are compatible with PAM-relaxed SpCas9-NG variant, enabling accurate correction of pathogenic mutations in homopolymeric cytosine sites through flexible positioning of the single-guide RNAs. Dual adeno-associated virus delivery of one haA3A-CBE variant to a mouse model of tyrosinemia induced up to 58.1% editing in liver tissues with minimal bystander editing, which was further reduced through single dose of lipid nanoparticle-based messenger RNA delivery of haA3A-CBEs. These results highlight the tremendous promise of haA3A-CBEs for precise genome editing to treat human diseases.

Engineering of efficiency-enhanced Cas9 and base editors with improved gene therapy efficacies.

Editing efficiency is pivotal for the efficacies of CRISPR-based gene therapies. We found that fusing an HMG-D domain to the N terminus of SpCas9 (named efficiency-enhanced Cas9 [eeCas9]) significantly increased editing efficiency by 1.4-fold on average. The HMG-D domain also enhanced the activities of non-NGG PAM Cas9 variants, high-fidelity Cas9 variants, smaller Cas9 orthologs, Cas9-based epigenetic regulators, and base editors in cell lines. Furthermore, we discovered that eeCas9 exhibits comparable off-targeting effects with Cas9, and its specificity could be increased through ribonucleoprotein delivery or using hairpin single-guide RNAs and high-fidelity Cas9s. The entire eeCas9 could be packaged into an adeno-associated virus vector and exhibited a 1.7- to 2.6-fold increase in editing efficiency targeting the Pcsk9 gene in mice, leading to a greater reduction of serum cholesterol levels. Moreover, the efficiency of eeA3A-BE3 also surpasses that of A3A-BE3 in targeting the promoter region of γ-globin genes or BCL11A enhancer in human hematopoietic stem cells to reactivate γ-globin expression for the treatment of ß-hemoglobinopathy. Together, eeCas9 and its derivatives are promising editing tools that exhibit higher activity and therapeutic efficacy for both in vivo and ex vivo therapeutics.

Amelioration of an Inherited Metabolic Liver Disease through Creation of a De Novo Start Codon by Cytidine Base Editing.

Base editing technology efficiently generates nucleotide conversions without inducing excessive double-strand breaks (DSBs), which makes it a promising approach for genetic disease therapy. In this study, we generated a novel hereditary tyrosinemia type 1 (HT1) mouse model, which contains a start codon mutation in the fumarylacetoacetate hydrolase (Fah) gene by using an adenine base editor (ABE7.10). To investigate the feasibility of base editing for recombinant adeno-associated virus (rAAV)-mediated gene therapy, an intein-split cytosine base editor (BE4max) was developed. BE4max efficiently induced C-to-T conversion and restored the start codon to ameliorate HT1 in mice, but an undesired bystander mutation abolished the effect of on-target editing. To solve this problem, an upstream sequence was targeted to generate a de novo in-frame start codon to initiate the translation of FAH. After treatment, almost all C-to-T conversions created a start codon and restored Fah expression, which efficiently ameliorated the disease without inducing off-target mutations. Our study demonstrated that base editing-mediated creation of de novo functional elements would be an applicable new strategy for genetic disease therapy.

Cas9-nickase-mediated genome editing corrects hereditary tyrosinemia in rats.

Hereditary tyrosinemia type I (HTI) is a metabolic genetic disorder caused by mutation of fumarylacetoacetate hydrolase (FAH). Because of the accumulation of toxic metabolites, HTI causes severe liver cirrhosis, liver failure, and even hepatocellular carcinoma. HTI is an ideal model for gene therapy, and several strategies have been shown to ameliorate HTI symptoms in animal models. Although CRISPR/Cas9-mediated genome editing is able to correct the Fah mutation in mouse models, WT Cas9 induces numerous undesired mutations that have raised safety concerns for clinical applications. To develop a new method for gene correction with high fidelity, we generated a Fah mutant rat model to investigate whether Cas9 nickase (Cas9n)-mediated genome editing can efficiently correct the Fah First, we confirmed that Cas9n rarely induces indels in both on-target and off-target sites in cell lines. Using WT Cas9 as a positive control, we delivered Cas9n and the repair donor template/single guide (sg)RNA through adenoviral vectors into HTI rats. Analyses of the initial genome editing efficiency indicated that only WT Cas9 but not Cas9n causes indels at the on-target site in the liver tissue. After receiving either Cas9n or WT Cas9-mediated gene correction therapy, HTI rats gained weight steadily and survived. Fah-expressing hepatocytes occupied over 95% of the liver tissue 9 months after the treatment. Moreover, CRISPR/Cas9-mediated gene therapy prevented the progression of liver cirrhosis, a phenotype that could not be recapitulated in the HTI mouse model. These results strongly suggest that Cas9n-mediated genome editing is a valuable and safe gene therapy strategy for this genetic disease.

Lipid nanoparticle-mediated base-editing of the Hao1 gene achieves sustainable primary hyperoxaluria type 1 therapy in rats.

Primary hyperoxaluria type 1 (PH1) is a severe hereditary disease, leading to the accumulation of oxalate in multiple organs, particularly the kidney. Hydroxyacid oxidase 1 (HAO1), a pivotal gene involved in oxalate production, is an approved target for the treatment of PH1. In this study, we demonstrated the discovery of several novel therapeutic sites of the Hao1 gene and the efficient editing of Hao1 c.290-2 A in vivo with lipid nanoparticles (LNP) delivered adenine base editing (ABE) mRNA. A single infusion of LNP-ABE resulted in a near-complete knockout of Hao1 in the liver, leading to the sustainable normalization of urinary oxalate (for at least 6 months) and complete rescue of the patho-physiology in PH1 rats. Additionally, a significant correlation between Hao1 editing efficiency and urinary oxalate levels was observed and over 60% Hao1 editing efficiency was required to achieve the normalization of urinary oxalate in PH1 rats. These findings suggest that the LNP-mediated base-editing of Hao1 c.290-2 A is an efficient and safe approach to PH1 therapy, highlighting its potential utility in clinical settings.

A de novo missense mutation in MPP2 confers an increased risk of Vogt-Koyanagi-Harada disease as shown by trio-based whole-exome sequencing.

Vogt-Koyanagi-Harada (VKH) disease is a leading cause of blindness in young and middle-aged people. However, the etiology of VKH disease remains unclear. Here, we performed the first trio-based whole-exome sequencing study, which enrolled 25 VKH patients and 50 controls, followed by a study of 2081 VKH patients from a Han Chinese population to uncover detrimental mutations. A total of 15 de novo mutations in VKH patients were identified, with one of the most important being the membrane palmitoylated protein 2 (MPP2) p.K315N (MPP2-N315) mutation. The MPP2-N315 mutation was highly deleterious according to bioinformatic predictions. Additionally, this mutation appears rare, being absent from the 1000 Genome Project and Genome Aggregation Database, and it is highly conserved in 10 species, including humans and mice. Subsequent studies showed that pathological phenotypes and retinal vascular leakage were aggravated in MPP2-N315 mutation knock-in or MPP2-N315 adeno-associated virus-treated mice with experimental autoimmune uveitis (EAU). In vitro, we used clustered regularly interspaced short palindromic repeats (CRISPR‒Cas9) gene editing technology to delete intrinsic MPP2 before overexpressing wild-type MPP2 or MPP2-N315. Levels of cytokines, such as IL-1ß, IL-17E, and vascular endothelial growth factor A, were increased, and barrier function was destroyed in the MPP2-N315 mutant ARPE19 cells. Mechanistically, the MPP2-N315 mutation had a stronger ability to directly bind to ANXA2 than MPP2-K315, as shown by LC‒MS/MS and Co-IP, and resulted in activation of the ERK3/IL-17E pathway. Overall, our results demonstrated that the MPP2-K315N mutation may increase susceptibility to VKH disease.

Long-term effects and benefits of Helicobacter pylori eradication on the gastric mucosa in older individuals.

BACKGROUND: The current international consensus report indicated that all Helicobacter pylori (H. pylori)-positive patients should be treated. This study aimed to evaluate the long-term effects and benefits of H. pylori eradication on the gastric mucosa in the elderly population. METHODS: We performed a retrospective cohort study with 311 individuals aged ≥60 years, including 83 with persistent H. pylori infection (persistent group), 128 with successful H. pylori eradication (eradicated group), and 100 without H. pylori infection (control group). The results of endoscopy and mucosal histology were investigated at baseline and followed up for 5 and 10 years. RESULTS: In the 5 to 10-year follow-up, there was a significant difference in the atrophy score among the three groups (P < 0.001); however, no significant difference was observed in the intestinal metaplasia (IM) score (P > 0.05). There was no significant difference in the cumulative incidence of gastric neoplastic lesion (GNL) between the eradicated and persistent groups during the 5 to 10-year follow-up period (P > 0.05). The baseline IM score of patients with GNL was significantly higher than that of those without GNL in the eradicated and control groups (P < 0.05). In all patients with GNL, the mean interval time between baseline and diagnosis of GLN was more than 6 years. The severity of baseline mucosal IM (odds ratio: OR 3.092, 95% confidence interval [CI]: 1.690-5.655, P < 0.001) and H. pylori infection (OR: 2.413, 95%CI: 1.019-5.712, P = 0.045) significantly increased the risk for GNL. CONCLUSIONS: Older patients with a life expectancy of less than 5 to 10 years, especially those with moderate to severe gastric mucosal IM, may not benefit from the eradication of H. pylori to prevent gastric cancer.

Long-term correction of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration.

CRISPR/Cas9-mediated site-specific insertion of exogenous genes holds potential for clinical applications. However, it is still infeasible because homologous recombination (HR) is inefficient, especially for non-dividing cells. To overcome the challenge, we report that a homology-independent targeted integration (HITI) strategy is used for permanent integration of high-specificity-activity Factor IX variant (F9 Padua, R338L) at the albumin (Alb) locus in a novel hemophilia B (HB) rat model. The knock-in efficiency reaches 3.66%, as determined by droplet digital PCR (ddPCR). The clotting time is reduced to a normal level four weeks after treatment, and the circulating factor IX (FIX) level is gradually increased up to 52% of the normal level over nine months even after partial hepatectomy, demonstrating the amelioration of hemophilia. Through primer-extension-mediated sequencing (PEM-seq), no significant off-target effect is detected. This study not only provides a novel model for HB but also identifies a promising therapeutic approach for rare inherited diseases.

Enhanced genome editing to ameliorate a genetic metabolic liver disease through co-delivery of adeno-associated virus receptor.

Genome editing through adeno-associated viral (AAV) vectors is a promising gene therapy strategy for various diseases, especially genetic disorders. However, homologous recombination (HR) efficiency is extremely low in adult animal models. We assumed that increasing AAV transduction efficiency could increase genome editing activity, especially HR efficiency, for in vivo gene therapy. Firstly, a mouse phenylketonuria (PKU) model carrying a pathogenic R408W mutation in phenylalanine hydroxylase (Pah) was generated. Through co-delivery of the general AAV receptor (AAVR), we found that AAVR could dramatically increase AAV transduction efficiency in vitro and in vivo. Furthermore, co-delivery of SaCas9/sgRNA/donor templates with AAVR via AAV8 vectors increased indel rate over 2-fold and HR rate over 15-fold for the correction of the single mutation in PahR408W mice. Moreover, AAVR co-injection successfully increased the site-specific insertion rate of a 1.4 kb Pah cDNA by 11-fold, bringing the HR rate up to 7.3% without detectable global off-target effects. Insertion of Pah cDNA significantly decreased the Phe level and ameliorated PKU symptoms. This study demonstrates a novel strategy to dramatically increase AAV transduction which substantially enhanced in vivo genome editing efficiency in adult animal models, showing clinical potential for both conventional and genome editing-based gene therapy.

Sex-specific differences in blood lipids and lipid ratios in type 2 diabetic foot patients.

AIMS/INTRODUCTION: Few people have reported whether there are sex differences in blood lipids and lipid ratios in type 2 diabetic foot (T2DF) patients in China. This study attempts to identify the contribution to sex-specific differences in blood lipids and lipid ratios in these patients. MATERIALS AND METHODS: In this case-control study, we explore 306 patients with T2DF as the study group and 306 patients with type 2 diabetes mellitus as the control group. Patients were diagnosed according to the Standards of Medical Care in Diabetes-2014 (American Diabetes Association). Blood lipid and lipid ratios were determined according to the National Cholesterol Education Program Adult Treatment Panel III criteria. RESULTS: We studied male patients with T2DF who were aged 68.00 years (18.00 years) and females who were aged 73.50 years (19.00 years); 61.76% of the patients were men. Men had higher body mass index and glycated hemoglobin levels than women. Compared with type 2 diabetes mellitus patients, T2DF patients had significant differences in total cholesterol/high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol/HDL-C and apolipoprotein (apo)B/apoA-I ratios. HDL-C, triglyceride, apoA-I and apoB/apoA-I ratio showed cardiovascular disease risk in men, whereas total cholesterol, low-density lipoprotein cholesterol, apoB, and the low-density lipoprotein cholesterol/HDL-C and total cholesterol/HDL-C ratios were better predictors in women. The apoB/apoA-I ratio odds ratio values were 2.18 (95% confidence interval 1.17-4.41) and 2.14 (95% confidence interval 1.14-4.00) in male patients with T2DF before and after adjusting for age, respectively (P < 0.05). CONCLUSIONS: T2DF patients present sex-specific differences in their blood lipid and lipid ratios, especially in the apoB/apoA-I ratio, which could be a better indicator for cardiovascular disease risk.

Design and tailoring of two-dimensional Schottky, PN and tunnelling junctions for electronics and optoelectronics.

Owing to their superior carrier mobility, strong light-matter interactions, and flexibility at the atomically thin thickness, two-dimensional (2D) materials are attracting wide interest for application in electronic and optoelectronic devices, including rectifying diodes, transistors, memory, photodetectors, and light-emitting diodes. At the heart of these devices, Schottky, PN, and tunneling junctions are playing an essential role in defining device function. Intriguingly, the ultrathin thickness and unique van der Waals (vdW) interlayer coupling in 2D materials has rendered enormous opportunities for the design and tailoring of various 2D junctions, e.g. using Lego-like hetero-stacking, surface decoration, and field-effect modulation methods. Such flexibility has led to marvelous breakthroughs during the exploration of 2D electronics and optoelectronic devices. To advance further, it is imperative to provide an overview of existing strategies for the engineering of various 2D junctions for their integration in the future. Thus, in this review, we provide a comprehensive survey of previous efforts toward 2D Schottky, PN, and tunneling junctions, and the functional devices built from them. Though these junctions exhibit similar configurations, distinct strategies have been developed for their optimal figures of merit based on their working principles and functional purposes.

Clinical research on liver reserve function by 13C-phenylalanine breath test in aged patients with chronic liver diseases.

BACKGROUND: The objective of this study was to investigate whether the 13C-phenylalanine breath test could be useful for the evaluation of hepatic function in elderly volunteers and patients with chronic hepatitis B and liver cirrhosis. METHODS: L-[1-13C] phenylalanine was administered orally at a dose of 100 mg to 55 elderly patients with liver cirrhosis, 30 patients with chronic hepatitis B and 38 elderly healthy subjects. The breath test was performed at 8 different time points (0, 10, 20, 30, 45, 60, 90, 120 min) to obtain the values of Delta over baseline, percentage 13CO2 exhalation rate and cumulative excretion (Cum). The relationships of the cumulative excretion with the 13C-%dose/h and blood biochemical parameters were investigated. RESULTS: The 13C-%dose/h at 20 min and 30 min combined with the cumulative excretion at 60 min and 120 min correlated with hepatic function tests, serum albumin, hemoglobin, platelet and Child-Pugh score. Prothrombin time, total and direct bilirubin were significantly increased, while serum albumin, hemoglobin and platelet, the cumulative excretion at 60 min and 120 min values decreased by degrees of intensity of the disease in Child-Pugh A, B, and C patients (P < 0.01). CONCLUSIONS: The 13C-phenylalanine breath test can be used as a non-invasive assay to evaluate hepatic function in elderly patients with liver cirrhosis. The 13C-%dose/h at 20 min, at 30 min and cumulative excretion at 60 min may be the key value for determination at a single time-point. 13C-phenylalanine breath test is safe and helpful in distinguishing different stages of hepatic dysfunction for elderly cirrhosis patients.

Optimization of Application Conditions of Drag Reduction Agent in Product Oil Pipelines.

Drag reduction performance was studied with a rotating disk instrument in the laboratory, and experiments show that there is an initial rapid growth stage and stability stage for drag reduction ratio change. The higher the rotational speed, the larger the initial drag reduction ratio is; the larger the concentration, the shorter the drag reduction stabilization time is. Under high concentration and high speed, the drag reduction onset time is short. Because of the shear degradation, the Reynolds number should be taken into account during use. Through a comparison of diesel properties after adding agents with national standard, it is confirmed that drag reduction agents could be used in this pipeline.

Increasing the efficiency and targeting range of cytidine base editors through fusion of a single-stranded DNA-binding protein domain.

Cytidine base editors are powerful genetic tools that catalyse cytidine to thymidine conversion at specific genomic loci, and further improvement of the editing range and efficiency is critical for their broader applications. Through insertion of a non-sequence-specific single-stranded DNA-binding domain from Rad51 protein between Cas9 nickase and the deaminases, serial hyper cytidine base editors were generated with substantially increased activity and an expanded editing window towards the protospacer adjacent motif in both cell lines and mouse embryos. Additionally, hyeA3A-BE4max selectively catalysed cytidine conversion in TC motifs with a broader editing range and much higher activity (up to 257-fold) compared with eA3A-BE4max. Moreover, hyeA3A-BE4max specifically generated a C-to-T conversion without inducing bystander mutations in the haemoglobin gamma gene promoter to mimic a naturally occurring genetic variant for amelioration of ß-haemoglobinopathy, suggesting the therapeutic potential of the improved base editors.

Dual base editor catalyzes both cytosine and adenine base conversions in human cells.

Although base editors are useful tools for precise genome editing, current base editors can only convert either adenines or cytosines. We developed a dual adenine and cytosine base editor (A&C-BEmax) by fusing both deaminases with a Cas9 nickase to achieve C-to-T and A-to-G conversions at the same target site. Compared to single base editors, A&C-BEmax's activity on adenines is slightly reduced, whereas activity on cytosines is higher and RNA off-target activity is substantially decreased.

Correction to: Increasing targeting scope of adenosine base editors in mouse and rat embryos through fusion of TadA deaminase with Cas9 variants.

In the original publication the grant number is incorrectly published. The correct grant number should be read as "17140901600". The corrected contents are provided in this correction article. This work was partially supported by grants from the National Natural Science Foundation of China (Nos. 81670470 and 81600149), a grant from the Shanghai Municipal Commission for Science and Technology (17140901600, 18411953500 and 15JC1400201) and a grant from National Key Research and Development Program (2016YFC0905100).

Effect of posture on (13)C-urea breath test in partial gastrectomy patients.

AIM: To investigate whether posture affects the accuracy of (13)C-urea breath test ((13)C-UBT) for Helicobacter pylori (H. pylori) detection in partial gastrectomy patients. METHODS: We studied 156 consecutive residual stomach patients, including 76 with H. pylori infection (infection group) and 80 without H. pylori infection (control group). H. pylori infection was confirmed if both the rapid urease test and histology were positive during gastroscopy. The two groups were divided into four subgroups according to patients' posture during the (13)C-UBT: subgroup A, sitting position; subgroup B, supine position; subgroup C, right lateral recumbent position; and subgroup D, left lateral recumbent position. Each subject underwent the following modified (13)C-UBT: 75 mg of (13)C-urea (powder) in 100 mL of citric acid solution was administered, and a mouth wash was performed immediately; breath samples were then collected at baseline and at 5-min intervals up to 30 min while the position was maintained. Seven breath samples were collected for each subject. The cutoff value was 2.0‰. RESULTS: The mean delta over baseline (DOB) values in the subgroups of the infection group were similar at 5 min (P > 0.05) and significantly higher than those in the corresponding control subgroups at all time points (P < 0.01). In the infection group, the mean DOB values in subgroup A were higher than those in other subgroups within 10 min and peaked at the 10-min point (12.4‰ ± 2.4‰). The values in subgroups B and C both reached their peaks at 15 min (B, 13.9‰ ± 1.5‰; C, 12.2‰ ± 1.7‰) and then decreased gradually until the 30-min point. In subgroup D, the value peaked at 20 min (14.7‰ ± 1.7‰). Significant differences were found between the values in subgroups D and B at both 25 min (t = 2.093, P = 0.043) and 30 min (t = 2.141, P = 0.039). At 30 min, the value in subgroup D was also significantly different from those in subgroups A and C (D vs C: t = 6.325, P = 0.000; D vs A: t = 5.912, P = 0.000). The mean DOB values of subjects with Billroth I anastomosis were higher than those of subjects with Billroth II anastomosis irrespectively of the detection time and posture (P > 0.05). CONCLUSION: Utilization of the left lateral recumbent position during the procedure and when collecting the last breath sample may improve the diagnostic accuracy of the (13)C-UBT in partial gastrectomy patients.