Boosting genome editing in plants with single transcript unit surrogate reporter systems

CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of edited events. In this study, we introduce multiple Single Transcript Unit Surrogate Reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems utilize the same sgRNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are employed to restore functional reporter genes post-genome editing, including efficient single strand annealing (SSA) for homologous recombination in STU-SR-SSA systems. STU-SR-BE systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are demonstrated to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.

PAM-Less CRISPR-SpRY Genome Editing in Plants

Engineered SpCas9 variant, SpRY, has been demonstrated to facilitate protospacer adjacent motif (PAM) unrestricted targeting of genomic DNA in various biological systems. Here we describe fast, efficient, and robust preparation of SpRY-derived genome and base editors that can be easily adapted to target various DNA sequences in plants due to modular Gateway assembly. Presented are detailed protocols for preparing T-DNA vectors for genome and base editors and for assessing genome editing efficiency through transient expression of these reagents in rice protoplasts.

[Characteristics and significance of outer retinal thickness changes in reticular macular disease]

Objective: To study the characteristics and significance of changes in the thickness of the outer retinal layer (ORL) outside the macula in patients with reticular macular disease (RMD). Methods: A cross-sectional study was conducted. The clinical data of patients who visited the Department of Ophthalmology of the First Affiliated Hospital of Guangzhou Medical University from February to September 2019 were retrospectively collected. Thirty-one patients with at least one eye (54 eyes in total) diagnosed with early/mid-stage age-related macular degeneration (AMD) were consecutively included in the AMD group, and 33 patients with at least one eye (64 eyes in total) showing subretinal wart-like deposits on optical coherence tomography images were consecutively included in the RMD group. Thirty-two volunteers aged between 50 to 90 years with a normal fundus in both eyes (64 eyes in total) were consecutively included in the healthy control (HC) group. Frequency domain optical coherence tomography was applied to examine and analyze the thickness features of the ORL, inner retinal layer and choroid at the macular fovea (F), 2 mm of the temporal edge (T), the nasal edge (N), the superior edge (S) and inferior edge (I) of the macular fovea in each group. The correlations of the thickness of ORL with the choroidal thickness and the blood flow density of the choriocapillaris layer in patients with RMD were also analyzed. Results: The thickness of ORL at the F, T, S and I sites in the RMD group was significantly thinner than that in the AMD and HC groups. The difference was most obvious at the F site [(90.27±8.93), (98.04±11.7) and (97.19±7.02)μm] in the RMD, AMD and HC groups, respectively; all P<0.01). In the logistic regression model with independent variables of the ORL thickness at the macular F site, gender and age, there was a significant association between the thickness of ORL at the F site and the incidence of RMD (odds ratio=0.926, P<0.05). The ORL and choroid in the eyes of patients with RMD were significantly thinner at the F site [(90.27±8.93) and (163.21±72.43) μm, respectively; both P<0.01] compared with the AMD [(98.04±11.7) and (235.34±64.15) μm, respectively] and HC [(97.19±7.02) and (240.08±62.27) μm, respectively] groups. However, the ORL and choroidal thickness did not show significant and strong linear correlations at multiple sites. In contrast, there was a significant linear correlation between the blood flow density of the choriocapillaris layer and the thickness of ORL at the F, T and S sites in patients with RMD (r=0.487, 0.722, 0.467, respectively; all P<0.05). Conclusions: The thickness of ORL outside the macula of eyes with RMD is thinner than that of healthy eyes and eyes with early/mid-stage AMD. The thinning of ORL outside the macula is related to the decrease in the blood flow density of the choriocapillaris layer in patients with RMD.

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice

PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that Cas9 nuclease and base editors, when coupled with the same guide RNA (gRNA), prefer distinct gRNA-dependent off-target sites. De novo generated gRNAs by SpRY editors lead to additional, but insubstantial, off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. ABE8e's preference for the TA motif is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scale and mechanisms of off-target and background mutations occurring during PAM-relaxed genome editing in plants.

Demirjian method and Willems method to study the dental age of adolescents in Shanghai before and after 10 years

BACKGROUND

The aim of this study is to assess the validity of whether the difference in dental age between 2009 to 2011 and 2021 is affected by environmental factors such as environmental pollution, floating population, and dietary habits. Demirjian and Willems dental age estimation methods were conducted for a Han population of children aged 8 to 14 in Shanghai, China. A total of 1,259 digital panorama radiographs of children aged 8.00-14.99 was estimated. All digital panorama radiographs were estimated using the Demirjian and Willems methods.

MATERIALS AND METHODS

Both 2009 to 2011 and 2021 were statistically analyzed by paired t-tests. The results show that the Demirjian method overestimates 2009 to 2011 and underestimates 2021 than children's chronological age. According to the Willms method, males are overestimated and females are underestimated from 2009 to 2011, and both genders were underestimated in 2021.

CONCLUSIONS

In conclusion, the difference in dental age between 2009 to 2011 and 2021 was statistically significant. Factors such as environment and dietary habits have been found to be affected by dental development. However, there are disputes among some researchers about the exact factors, so it is suggested to further study the effects of environmental factors on tooth development.

Improved plant cytosine base editors with high editing activity, purity, and specificity

Cytosine base editors (CBEs) are great additions to the expanding genome editing toolbox. To improve C-to-T base editing in plants, we first compared seven cytidine deaminases in the BE3-like configuration in rice. We found A3A/Y130F-CBE_V01 resulted in the highest C-to-T base editing efficiency in both rice and Arabidopsis. Furthermore, we demonstrated this A3A/Y130F cytidine deaminase could be used to improve iSpyMacCas9-mediated C-to-T base editing at A-rich PAMs. To showcase its applications, we first applied A3A/Y130F-CBE_V01 for multiplexed editing to generate microRNA-resistant mRNA transcripts as well as pre-mature stop codons in multiple seed trait genes. In addition, we harnessed A3A/Y130F-CBE_V01 for efficient artificial evolution of novel ALS and EPSPS alleles which conferred herbicide resistance in rice. To further improve C-to-T base editing, multiple CBE_V02, CBE_V03 and CBE_V04 systems were developed and tested in rice protoplasts. The CBE_V04 systems were found to have improved editing activity and purity with focal recruitment of more uracil DNA glycosylase inhibitors (UGIs) by the engineered single guide RNA 2.0 scaffold. Finally, we used whole-genome sequencing (WGS) to compare six CBE_V01 systems and four CBE_V04 systems for genome-wide off-target effects in rice. Different levels of cytidine deaminase-dependent and sgRNA-independent off-target effects were indeed revealed by WGS among edited lines by these CBE systems. We also investigated genome-wide sgRNA-dependent off-target effects by different CBEs in rice. This comprehensive study compared 21 different CBE systems, and benchmarked PmCDA1-CBE_V04 and A3A/Y130F-CBE_V04 as next-generation plant CBEs with high editing efficiency, purity, and specificity.

[Urinary retinol binding protein and β2-microglobulin were associated with urinary albumin to creatinine ratio and renal function in hospitalized diabetic patients]

Objective: To explore the associations of urinary retinol binding protein (RBP) and β₂-microglobulin (β₂-MG) with urinary albumin to creatinine ratio (UACR) and renal function in hospitalized patients with type 2 diabetes mellitus (T2DM). Methods: A total of 1 030 Chinese patients with T2DM were included in this study. The subjects were divided into the UACR normal group (<30 mg/g), microalbuminuria group (30-300 mg/g) and macroalbuminuria group (>300 mg/g). Patients with normal UACR were further divided into two groups according to the estimated glomerular filtration rate (eGFR): the eGFR low group (<90 ml·min^-1·1.73m^-2) and the normal eGFR group (≥90 ml·min^-1·1.73m^-2). Urine RBP and β₂-MG levels among the groups were compared. Multiple linear regression analyses were applied to evaluate risk factors of urine RBP and β₂-MG. Results: In all patients (n=1 030), urine RBP and β₂-MG increased gradually with the increase of UACR across the three groups, the proportions of abnormal urine RBP (>0.7 mg/L) and β₂-MG (>370 μg/L) in these groups were 3.8%, 8.5%, 39.0% (P<0.001), and 12.9%, 26.7%, 46.8% (P<0.001), respectively. In the UACR normal group (n=788), 12.2% of the patients were with eGFR<90 ml·min^-1·1.73m^-2. The proportion of abnormal β₂-MG (>370 μg/L) was higher in the eGFR low group than that in the eGFR normal group (29.2% vs. 10.7%, P<0.001). Multivariate linear stepwise regression analyses were performed using natural logarithm of urine RBP or β₂-MG as dependent variable, and showed that urine RBP was independently associated with UACR (β=0.0005, P<0.001), serum creatinine (β=0.006, P<0.001) and glycosylated hemoglobin A1c (β=0.050, P=0.001), and β₂-MG was independently correlated with UACR (β=0.000 4, P<0.001), serum creatinine (β=0.011, P<0.001), systolic blood pressure (β=0.005, P=0.031) and fasting blood-glucose (β=0.027, P=0.046). Conclusions: Urine RBP and β₂-MG are positively associated with high UACR and impaired renal function in T2DM patients, and these changes could occur before UACR and eGFR turned out to be abnormal. It is recommended that urine RBP and β₂-MG be detected as early as possible to identify diabetic kidney disease in patients with normal UACR and eGFR.

Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems

CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12a, we screen nine Cas12a orthologs that have not been demonstrated in plants, and identify six, ErCas12a, Lb5Cas12a, BsCas12a, Mb2Cas12a, TsCas12a and MbCas12a, that possess high editing activity in rice. Among them, Mb2Cas12a stands out with high editing efficiency and tolerance to low temperature. An engineered Mb2Cas12a-RVRR variant enables editing with more relaxed PAM requirements in rice, yielding two times higher genome coverage than the wild type SpCas9. To enable large-scale genome engineering, we compare 12 multiplexed Cas12a systems and identify a potent system that exhibits nearly 100% biallelic editing efficiency with the ability to target as many as 16 sites in rice. This is the highest level of multiplex edits in plants to date using Cas12a. Two compact single transcript unit CRISPR-Cas12a interference systems are also developed for multi-gene repression in rice and Arabidopsis. This study greatly expands the targeting scope of Cas12a for crop genome engineering.

Thermo-Responsive Shape Memory Behavior of Methyl Vinyl Silicone Rubber/Olefin Block Copolymer Blends via Co-Crosslinking

Shape memory polymers (SMPs) are developed by blending and cross-linking polymers which include crystalline domains and cross-linked networks. In this paper, we describe the morphology, thermal and shape memory behavior of methyl vinyl silicone rubber (MVMQ)/olefin block copolymer (OBC) blends prepared by a melt-blending and chemical cross-linking method. MVMQ without crystalline domains could not hold its temporary shape. After introducing the OBC, the obtained blends exhibited excellent dual shape memory properties. The cross-linking networks of MVMQ acted as reversible domains, while crystalline regions of OBC worked as fixed domains. When the blending ratio of MVMQ/OBC was 50/ 50, the blend had both a high shape fixity ratio and shape recovery ratio.

Orbital competition of Mn3+ and V3+ ions in Mn1+x V2-x O4

The structural and magnetic properties of Mn1+x V2-x O4 (0 < x ⩽ 1) have been investigated by the heat capacity, magnetization, x-ray diffraction and neutron diffraction measurements, and a phase diagram of temperature versus composition was built up. For x ⩽ 0.3, a cubic-to-tetragonal (c > a) phase transition was observed. For x > 0.3, the system maintained the tetragonal lattice. Although the collinear and noncollinear magnetic transitions of V3+ ions were obtained in all compositions, the canting angles between the V3+ ions decreased with Mn3+-doping, and the ordering of the Mn3+ ions was only observed as x > 0.4. In order to study the dynamics of the ground state, the first principles simulation was applied to analyze not only the orbital effects of Mn2+, Mn3+, and V3+ ions, but also the related exchange energies.

PAM-less plant genome editing using a CRISPR-SpRY toolbox

The rapid development of the CRISPR-Cas9, -Cas12a and -Cas12b genome editing systems has greatly fuelled basic and translational plant research^1-6. DNA targeting by these Cas nucleases is restricted by their preferred protospacer adjacent motifs (PAMs). The PAM requirement for the most popular Streptococcus pyogenes Cas9 (SpCas9) is NGG (N = A, T, C, G)⁷, limiting its targeting scope to GC-rich regions. Here, we demonstrate genome editing at relaxed PAM sites in rice (a monocot) and the Dahurian larch (a coniferous tree), using an engineered SpRY Cas9 variant⁸. Highly efficient targeted mutagenesis can be readily achieved by SpRY at relaxed PAM sites in the Dahurian larch protoplasts and in rice transgenic lines through non-homologous end joining (NHEJ). Furthermore, an SpRY-based cytosine base editor was developed and demonstrated by directed evolution of new herbicide resistant OsALS alleles in rice. Similarly, a highly active SpRY adenine base editor was developed based on ABE8e (ref. ⁹) and SpRY-ABE8e was able to target relaxed PAM sites in rice plants, achieving up to 79% editing efficiency with high product purity. Thus, the SpRY toolbox breaks a PAM restriction barrier in plant genome engineering by enabling DNA editing in a PAM-less fashion. Evidence was also provided for secondary off-target effects by de novo generated single guide RNAs (sgRNAs) due to SpRY-mediated transfer DNA self-editing, which calls for more sophisticated programmes for designing highly specific sgRNAs when implementing the SpRY genome editing toolbox.

Biology and applications of Clonostachys rosea

Clonostachys rosea is a promising saprophytic filamentous fungus that belongs to phylum Ascomycota. Clonostachys rosea is widespread around the world and exists in many kinds of habitats, with the highest frequency in soil. As an excellent mycoparasite, C. rosea exhibits strong biological control ability against numerous fungal plant pathogens, nematodes and insects. These behaviours are based on the activation of multiple mechanisms such as secreted cell-wall-degrading enzymes, production of antifungal secondary metabolites and induction of plant defence systems. Besides having significant biocontrol activity, C. rosea also functions in the biodegradation of plastic waste, biotransformation of bioactive compounds, as a bioenergy sources and in fermentation. This mini review summarizes information about the biology and various applications of C. rosea and expands on its possible uses.

CRISPR-Cas12b enables efficient plant genome engineering

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12b is a newly emerged genome engineering system. Here, we compared Cas12b from Alicyclobacillus acidoterrestris (Aac), Alicyclobacillus acidiphilus (Aa), Bacillus thermoamylovorans (Bth) and Bacillus hisashii (Bh) for genome engineering in rice, an important crop. We found AaCas12b was more efficient than AacCas12b and BthCas12b for targeted mutagenesis, which was further demonstrated in multiplexed genome editing. We also engineered the Cas12b systems for targeted transcriptional repression and activation. Our work establishes Cas12b as the third promising CRISPR system, after Cas9 and Cas12a, for plant genome engineering.

Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

BACKGROUND

Expression of either Cas9 or Cas12a and guide RNAs by a single Polymerase II (Pol II) promoter represents a compact CRISPR expression system and has many advantages for different applications. In order to make this system routine in plant biology, engineering efforts are needed for developing and optimizing such single transcript unit (STU) systems for plant genome editing.

RESULTS

To develop novel intron-based STU (iSTU) CRISPR system (STU CRISPR 3.0), we first evaluated three introns from three plant species for carrying guide RNAs by using an enhanced green fluorescence protein (eGFP) system in rice. After validation of proper intron slicing, we inserted these gRNA-containing introns into the open reading frames (ORFs) of Cas9 and Cas12a for testing their genome editing capability. Different guide RNA processing strategies have been tested for Cas9 and Cas12a. We demonstrated singular genome editing and multiplexed genome editing with these iSTU-Cas9 and iSTU-Cas12a systems.

CONCLUSION

We developed multiple iSTU-CRISPR/Cas9 and Cas12a systems for plant genome editing. Our results shed light on potential directions for further improvement of the iSTU systems.

[Spectomycin B1 induces VEGFR2 de-SUMO modification to inhibit angiogenesis in nasopharyngeal carcinoma]

Objective:To explore the new mechanism of spectomycin B1 in inhibiting angiogenesis of nasopharyngeal carcinoma and to provide a theoretical basis for targeted gene therapy of nasopharyngeal carcinoma. Method:Human nasopharyngeal carcinoma CNE1 cells were divided into two groups, the control group and spectomycin B1 group. Western blot was used to detect the expression levels of small ubiquitin-related modified protein（SUMO） 1 and vascular endothelial growth factor receptor 2（VEGFR2）. The angiogenesis assay was used to detect the angiogenic ability of CNE1 cells, and the apoptosis was detected by flow cytometry. The model of nasopharyngeal carcinoma-bearing mice was established, spectomycin B1 was administered, tumor volume and weight were measured, and protein expression of CD31 was detected by immunohistochemistry and microvessel density was compared. Result:Spectomycin B1 could reduce deSUMOylation of VEGFR2 protein by 4.05 times, significantly reduce the angiogenic ability of CNE1 cells, and increase the apoptosis rate by 20.68%. In the tumor-bearing mouse model, spectomycin B1 treatment could inhibit subcutaneous tumor growth rate and weight, and the blood vessel density decreased by 40.04%. Conclusion:Spectomycin B1 can inhibit neovascularization of nasopharyngeal carcinoma by inducing deSUMOylation of VEGFR2 protein.

Chronic peripheral ghrelin injection exerts antifibrotic effects by increasing growth differentiation factor 15 in rat hearts with myocardial fibrosis induced by isoproterenol

This study aimed to investigate the anti-fibrotic effects of ghrelin in isoproterenol (ISO)-induced myocardial fibrosis and the underlying mechanism. Sprague-Dawley rats were randomized to control, ISO, and ISO + ghrelin groups. ISO (2 mg/kg per day, subcutaneous) or vehicle was administered once daily for 7 days, then ghrelin (100 microg/kg per day, subcutaneous) was administered once daily for the next 3 weeks. Ghrelin treatment greatly improved the cardiac function of ISO-treated rats. Ghrelin also decreased plasma brain natriuretic peptide level and ratios of heart weight to body weight and left ventricular weight to body weight. Ghrelin significantly reduced myocardial collagen area and hydroxyproline content, accompanied by decreased mRNA levels of collagen type I and III. Furthermore, ghrelin increased plasma level of growth differentiation factor 15 (GDF15) and GDF15 mRNA and protein levels in heart tissues, which were significantly decreased with ISO alone. The phosphorylation of Akt at Ser473 and GSK-3beta at Ser9 was decreased with ISO, and ghrelin significantly reversed the downregulation of p-Akt and p-GSK-3beta. Mediated by GDF15, ghrelin could attenuate ISO-induced myocardial fibrosis via Akt-GSK-3beta signaling.

Genetic determinates for conjugated linolenic acid production in Lactobacillus plantarum ZS2058

AIMS

To investigate the genetic determinates for conjugated linolenic acid (CLNA) production in Lactobacillus plantarum ZS2058, a high CLNA producer.

METHODS AND RESULTS

After culturing with α-linolenic acid (ALA) in the medium, the fatty acid compositions of supernatant fluid and cell pellets were analysed via GC-MS. cis9,trans11,cis15-CLNA was identified to be the predominant isomer. And during CLNA production, 10-hydroxy-cis12-cis15-octadecenoic acid (10-HOEA) and 10-oxo-cis12-cis15-octadecenoic acid (10-OXOA) were accumulated. The E. coli recombinants harbouring genes encoding myosin-cross-reactive antigen (MCRA), short-chain dehydrogenase/oxidoreductase (DH) and acetoacetate decarboxylase (DC), respectively, were analysed for their roles in CLNA production. The results indicated that MCRA converted ALA to 10-HOEA, following converted to 10-OXOA by DH. While with the combination of three recombinants, ALA could be transformed into CLNA plus 10-HOEA and 10-OXOA. When the three genes were deleted, none of the L. plantarum ZS2058 knockout mutants could produce any CLNA, after complementation, and all the complementary mutants recovered the CLNA-production ability at similar levels as the wild strain.

CONCLUSIONS

Lactobacillus plantarum ZS2058 produced CLNA from ALA with 10-HOEA and 10-OXOA as intermediates. The triple-component isomerase of MCRA, DH and DC was the unique genetic determinant for CLNA generation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current results firstly provided conclusive evidence that the triple-component isomerase complex was shared by both CLA and CLNA production in lactobacilli.

Identification and comparative profiling of gonadal microRNAs in the adult pigeon (Columba livia)

1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.

[Hypoxia increases chemotherapy resistance in nasopharyngeal carcinoma via inducing CDK6 deSUMOylation]

Objective: To understand the mechanism of chemotherapy resistance in nasopharyngeal carcinoma under hypoxic conditions through the perspective of protein SUMOylation modification. Methods: Cobalt chloride (CoCl(2)) was used to establish the hypoxic model of human nasopharyngeal carcinoma CNE1 cells. Then, the cell cycle was detected by flow cytometry, and the expression level of small ubiquitin-related modifier(SUMO) and cyclin-dependent kinase 6 (CDK6) proteins were detected by western blotting. MTT assay was used to determine the median lethal dose (IC(50)) of cancer cells against cisplatin, and enzyme-linked immunosorbent assay (ELISA) was used to determine lactate dehydrogenase (LDH) level. Results: The cell cycle of CNE1 induced by hypoxia was arrested in G0/G1 phase.The results of Western blot showed that the protein expression level of CDK6 in CNE1 cells was lower than that in the control group (0.83±0.25 vs. 0.43±0.21, t=14.67, P=0.003). The protein level of conjugated SUMO1 was significantly lower than that in the control group (2.69±0.48 vs. 1.38±0.31, t=17.22, P=0.001), while the level of free SUMO1 protein was significantly higher than that in the control group (2.01±0.43 vs. 2.60±0.59, t=15.45, P=0.002).The LC50 of CNE1 cells in the control group was significantly lower than that in the hypoxic group (29.44 μg/ml vs. 97.72 μg/ml, t=12.79, P=0.001). After CNE1 cells received 50 μg/ml cisplatin for 48 h, the LDH content in the supernatant of the control group was significantly higher than that in the hypoxic group ((541.49±64.59) ng/ml vs. (234.67±41.03) ng/ml, t=11.94, P=0.007)). The apoptosis rate of CNE1 cells in the control group was significantly higher than that in the hypoxic group ((76.64±5.37)% vs. (32.84±4.77) ng/ml, t=8.49, P=0.003)). Conclusion: Hypoxia can dissociate the covalent modification of CDK6 and SUMO1, inhibit cell cycle and increase the chemotherapy resistance of nasopharyngeal carcinoma.

Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG

Two recently engineered SpCas9 variants, namely xCas9 and Cas9-NG, show promising potential in improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9-3.7, the most effective xCas9 variant in mammalian cells, for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates. xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested, whereas it showed limited activity at non-canonical NGH (H = A, C, T) PAM sites. High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBEC1 and PmCDA1 cytidine deaminases. With mismatched sgRNAs, we found that xCas9 had improved targeting specificity over the Cas9-WT. Furthermore, we tested two Cas9-NG variants, Cas9-NGv1 and Cas9-NG, for targeting NGN PAMs. Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested, and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT, GAA, and CAA. Nevertheless, we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites. In stable transgenic rice lines, we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites. To expand the base-editing scope, we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version), PmCDA1, and UGI. Taken together, our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.

Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing

CRISPR-Cas9 and Cas12a are two powerful genome editing systems. Expression of CRISPR in plants is typically achieved with a mixed dual promoter system, in which Cas protein is expressed by a Pol II promoter and a guide RNA is expressed by a species-specific Pol III promoter such as U6 or U3. To achieve coordinated expression and compact vector packaging, it is desirable to express both CRISPR components under a single Pol II promoter. Previously, we demonstrated a first-generation single transcript unit (STU)-Cas9 system, STU-Cas9-RZ, which is based on hammerhead ribozyme for processing single guide RNAs (sgRNAs). In this study, we developed two new STU-Cas9 systems and one STU-Cas12a system for applications in plants, collectively called the STU CRISPR 2.0 systems. We demonstrated these systems for genome editing in rice with both transient expression and stable transgenesis. The two STU-Cas9 2.0 systems process the sgRNAs with Csy4 ribonuclease and endogenous tRNA processing system respectively. Both STU-Cas9-Csy4 and STU-Cas9-tRNA systems showed more robust genome editing efficiencies than our first-generation STU-Cas9-RZ system and the conventional mixed dual promoter system. We further applied the STU-Cas9-tRNA system to compare two C to T base editing systems based on rAPOBEC1 and PmCDA1 cytidine deaminases. The results suggest STU-based PmCDA1 base editor system is highly efficient in rice. The STU-Cas12a system, based on Cas12a' self-processing of a CRISPR RNA (crRNA) array, was also developed and demonstrated for expression of a single crRNA and four crRNAs. Altogether, our STU CRISPR 2.0 systems further expanded the CRISPR toolbox for plant genome editing and other applications.

Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis

BACKGROUND

CRISPR-Cas12a (formerly Cpf1) is an RNA-guided endonuclease with distinct features that have expanded genome editing capabilities. Cas12a-mediated genome editing is temperature sensitive in plants, but a lack of a comprehensive understanding on Cas12a temperature sensitivity in plant cells has hampered effective application of Cas12a nucleases in plant genome editing.

RESULTS

We compared AsCas12a, FnCas12a, and LbCas12a for their editing efficiencies and non-homologous end joining (NHEJ) repair profiles at four different temperatures in rice. We found that AsCas12a is more sensitive to temperature and that it requires a temperature of over 28 °C for high activity. Each Cas12a nuclease exhibited distinct indel mutation profiles which were not affected by temperatures. For the first time, we successfully applied AsCas12a for generating rice mutants with high frequencies up to 93% among T0 lines. We next pursued editing in the dicot model plant Arabidopsis, for which Cas12a-based genome editing has not been previously demonstrated. While LbCas12a barely showed any editing activity at 22 °C, its editing activity was rescued by growing the transgenic plants at 29 °C. With an early high-temperature treatment regime, we successfully achieved germline editing at the two target genes, GL2 and TT4, in Arabidopsis transgenic lines. We then used high-temperature treatment to improve Cas12a-mediated genome editing in maize. By growing LbCas12a T0 maize lines at 28 °C, we obtained Cas12a-edited mutants at frequencies up to 100% in the T1 generation. Finally, we demonstrated DNA binding of Cas12a was not abolished at lower temperatures by using a dCas12a-SRDX-based transcriptional repression system in Arabidopsis.

CONCLUSION

Our study demonstrates the use of high-temperature regimes to achieve high editing efficiencies with Cas12a systems in rice, Arabidopsis, and maize and sheds light on the mechanism of temperature sensitivity for Cas12a in plants.

Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing

CRISPR-Cas systems can be expressed in multiple ways, with different capabilities regarding tissue-specific expression, efficiency, and expression levels. Thus far, three expression strategies have been demonstrated in plants: mixed dual promoter systems, dual Pol II promoter systems, and single transcript unit (STU) systems. We explored a fourth strategy to express CRISPR-Cas9 in the model and crop plant, rice, where a bidirectional promoter (BiP) is used to express Cas9 and single guide RNA (sgRNA) in opposite directions. We first tested an engineered BiP system based on double-mini 35S promoter and an Arabidopsis enhancer, which resulted in 20.7% and 52.9% genome editing efficiencies at two target sites in T0 stable transgenic rice plants. We further improved the BiP system drastically by using a rice endogenous BiP, OsBiP1. The endogenous BiP expression system had higher expression strength and led to 75.9-93.3% genome editing efficiencies in rice T0 generation, when the sgRNAs were processed by either tRNA or Csy4. We provided a proof-of-concept study of applying BiP systems for expressing two-component CRISPR-Cas9 genome editing reagents in rice. Our work could promote future research and adoption of BiP systems for CRISPR-Cas-based genome engineering in plants.

A Single Transcript CRISPR-Cas9 System for Multiplex Genome Editing in Plants

The CRISPR-Cas9 system has been widely adopted in genome editing. By changing the 20 bp guide sequence, it can easily edit any sequence adjacent to a protospacer adjacent motif (PAM) in a genome. Multiplex genome editing could be accomplished with simultaneous expression of multiple single-guide RNAs (sgRNA). Given that sgRNAs are expressed by Pol III promoters, multiplex genome editing is conventionally done by assembly of multiple complete sgRNA expression cassettes together, which can be a challenge in vector construction. Here, we described a multiplex genome editing system based on a single transcript unit CRISPR-Cas9 (STU CRISPR-Cas9) expression system driven by a single Pol II promoter. It represents a novel approach for multiplex genome editing.

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice

BACKGROUND

Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date.

RESULTS

We conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice. The sequencing depths range from 45× to 105× with read mapping rates above 96%. Our results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and three Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation.

CONCLUSIONS

Our comprehensive and rigorous analysis of WGS data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice

BACKGROUND

Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date.

RESULTS

We conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice. The sequencing depths range from 45× to 105× with read mapping rates above 96%. Our results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and three Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation.

CONCLUSIONS

Our comprehensive and rigorous analysis of WGS data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.

CRISPRMatch: An Automatic Calculation and Visualization Tool for High-throughput CRISPR Genome-editing Data Analysis

Custom-designed nucleases, including CRISPR-Cas9 and CRISPR-Cpf1, are widely used to realize the precise genome editing. The high-coverage, low-cost and quantifiability make high-throughput sequencing (NGS) to be an effective method to assess the efficiency of custom-designed nucleases. However, contrast to standardized transcriptome protocol, the NGS data lacks a user-friendly pipeline connecting different tools that can automatically calculate mutation, evaluate editing efficiency and realize in a more comprehensive dataset that can be visualized. Here, we have developed an automatic stand-alone toolkit based on python script, namely CRISPRMatch, to process the high-throughput genome-editing data of CRISPR nuclease transformed protoplasts by integrating analysis steps like mapping reads and normalizing reads count, calculating mutation frequency (deletion and insertion), evaluating efficiency and accuracy of genome-editing, and visualizing the results (tables and figures). Both of CRISPR-Cas9 and CRISPR-Cpf1 nucleases are supported by CRISPRMatch toolkit and the integrated code has been released on GitHub (https://github.com/zhangtaolab/CRISPRMatch).

Optimization of Growth Temperature of β-Ga₂O₃ Thin Films for Solar-Blind Photodetectors

Monoclinic gallium oxide thin films were deposited on c-plane sapphire substrates at various substrate temperatures ranging from 450 °C to 700 °C by radio frequency magnetron sputtering technology. X-ray diffraction results showed that the deposited β-Ga2O3 films were oriented at ( 2 ¯ 01) direction. As the substrate temperature increased, the intensity of β-Ga2O3 peaks increased and bandgap decreased accordingly. Metal/semiconductor/metal structured solar-blind photodetectors based on β-Ga2O3 thin films growing at various substrate temperatures had been fabricated. The growth temperatures of thin films had no obvious influence on dark current and response to 365 nm light illuminations. The photoelectric properties such as responsivity and response speed of the thin films to 254 nm light illuminations were growth temperature dependent. At an applied bias of 50 V, the photodetectors prepared with 450 °C grown film had the highest responsivity of 2.18 A/W, and the photodetectors prepared with 700 °C grown film had the shortest rising time of 0.95 s under 254 nm light illuminations.

Effects of bone morphogenetic protein-2 (BMP-2) and vascular endothelial growth factor (VEGF) release from polylactide-poly (ethylene glycol)-polylactide (PELA) microcapsule-based scaffolds on bone

Multiple growth factors can be administered to mimic the natural process of bone healing in bone tissue engineering. We investigated the effects of sequential release of bone morphogenetic protein-2 (BMP-2) and vascular endothelial growth factor (VEGF) from polylactide-poly (ethylene glycol)-polylactide (PELA) microcapsule-based scaffolds on bone regeneration. To improve the double emulsion/solvent evaporation technique, VEGF was encapsulated in PELA microcapsules, to which BMP-2 was attached. The scaffold (BMP-2/PELA/VEGF) was then fused to these microcapsules using the dichloromethane vapor method. The bioactivity of the released BMP-2 and VEGF was then quantified in rat mesenchymal stem cells (rMSCs). Immunoblotting analysis showed that BMP-2/PELA/VEG promoted the differentiation of rMSCs into osteoblasts via the MAPK and Wnt pathways. Osteoblast differentiation was assessed through alkaline phosphatase expression. When compared with simple BMP-2 plus VEGF group and pure PELA group, osteoblast differentiation in BMP-2/PELA/VEGF group significantly increased. An MTT assay indicated that BMP-2-loaded PELA scaffolds had no adverse effects on cell activity. BMP-2/PELA/VEG promoted the differentiation of rMSCs into osteoblast via the ERK1/2 and Wnt pathways. Our findings indicate that the sequential release of BMP-2 and VEGF from PELA microcapsule-based scaffolds is a promising approach for the treatment of bone defects.

A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants

This corrects the article DOI: 10.1038/nplants.2017.18.

A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants

This corrects the article DOI: 10.1038/nplants.2017.18.

Altered expression of BDNF, BDNF pro-peptide and their precursor proBDNF in brain and liver tissues from psychiatric disorders: rethinking the brain-liver axis

Brain-derived neurotrophic factor (BDNF) has a role in the pathophysiology of psychiatric disorders. The precursor proBDNF is converted to mature BDNF and BDNF pro-peptide, the N-terminal fragment of proBDNF; however, the precise function of these proteins in psychiatric disorders is unknown. We sought to determine whether expression of these proteins is altered in the brain and peripheral tissues from patients with psychiatric disorders. We measured protein expression of proBDNF, mature BDNF and BDNF pro-peptide in the parietal cortex, cerebellum, liver and spleen from control, major depressive disorder (MDD), schizophrenia (SZ) and bipolar disorder (BD) groups. The levels of mature BDNF in the parietal cortex from MDD, SZ and BD groups were significantly lower than the control group, whereas the levels of BDNF pro-peptide in this area were significantly higher than controls. In contrast, the levels of proBDNF and BDNF pro-peptide in the cerebellum of MDD, SZ and BD groups were significantly lower than controls. Moreover, the levels of mature BDNF from the livers of MDD, SZ and BD groups were significantly higher than the control group. The levels of mature BDNF in the spleen did not differ among the four groups. Interestingly, there was a negative correlation between mature BDNF in the parietal cortex and mature BDNF in the liver in all the subjects. These findings suggest that abnormalities in the production of mature BDNF and BDNF pro-peptide in the brain and liver might have a role in the pathophysiology of psychiatric disorders, indicating a brain-liver axis in psychiatric disorders.

A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription. Our data suggest promising applications of CRISPR-Cpf1 for editing plant genomes and modulating the plant transcriptome.

Multidisciplinary Cooperation in a Simultaneous Combined Liver and Kidney Transplantation Patient of Primary Hyperoxaluria 1

Primary hyperoxaluria type 1 is an autosomal recessive hereditary glyoxylate metabolism disorder characterized by excessive production of oxalate, caused by the deficiency of liver specific peroxisomal enzyme: alanineglyoxylate aminotransferase. For patients with end-stage renal disease, combined liver and kidney transplantation was needed. This report describes one patient, with a diagnosis of end-stage renal disease and primary hyperoxaluria 1 confirmed by PCR and direct sequencing with genomic DNA, received the simultaneous combined liver and kidney transplantation after seven months' waiting. However, there were several complications observed post surgery, such as protracted bleeding, common bile duct anastomotic stenosis, biliary calculi and recurrence of urolithiasis. All these were well solved by relevant department, and finally a satisfactory outcome was achieved. Multidisciplinary cooperation plays an important role on the PH1 patient management, especially when multiple complications are encountered.