Can SpRY recognize any PAM in human cells? / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

The application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) can be limited due to a lack of compatible protospacer adjacent motif (PAM) sequences in the DNA regions of interest. Recently, SpRY, a variant of Streptococcus pyogenes Cas9 (SpCas9), was reported, which nearly completely fulfils the PAM requirement. Meanwhile, PAMs for SpRY have not been well addressed. In our previous study, we developed the PAM Definition by Observable Sequence Excision (PAM-DOSE) and green fluorescent protein (GFP)‍-reporter systems to study PAMs in human cells. Herein, we endeavored to identify the PAMs of SpRY with these two methods. The results indicated that 5'-NRN-3', 5'-NTA-3', and 5'-NCK-3' could be considered as canonical PAMs. 5'-NCA-3' and 5'-NTK-3' may serve as non-priority PAMs. At the same time, PAM of 5'-NYC-3' is not recommended for human cells. These findings provide further insights into the application of SpRY for human genome editing.

Single-copy Loss of Rho Guanine Nucleotide Exchange Factor 10 ( arhgef10) Causes Locomotor Abnormalities in Zebrafish Larvae / 生物医学与环境科学（英文）

OBJECTIVE@#To determine if ARHGEF10 has a haploinsufficient effect and provide evidence to evaluate the severity, if any, during prenatal consultation.@*METHODS@#Zebrafish was used as a model for generating mutant. The pattern of arhgef10 expression in the early stages of zebrafish development was observed using whole-mount in situ hybridization (WISH). CRISPR/Cas9 was applied to generate a zebrafish model with a single-copy or homozygous arhgef10 deletion. Activity and light/dark tests were performed in arhgef10 -/-, arhgef10 +/-, and wild-type zebrafish larvae. ARHGEF10 was knocked down using small interferon RNA (siRNA) in the SH-SY5Y cell line, and cell proliferation and apoptosis were determined using the CCK-8 assay and Annexin V/PI staining, respectively.@*RESULTS@#WISH showed that during zebrafish embryonic development arhgef10 was expressed in the midbrain and hindbrain at 36-72 h post-fertilization (hpf) and in the hemopoietic system at 36-48 hpf. The zebrafish larvae with single-copy and homozygous arhgef10 deletions had lower exercise capacity and poorer responses to environmental changes compared to wild-type zebrafish larvae. Moreover, arhgef10 -/- zebrafish had more severe symptoms than arhgef10 +/- zebrafish. Knockdown of ARHGEF10 in human neuroblastoma cells led to decreased cell proliferation and increased cell apoptosis.@*CONCLUSION@#Based on our findings, ARHGEF10 appeared to have a haploinsufficiency effect.

Structure-based optimization and design of CRISPR protein xCas9 / 生物工程学报

Streptococcus pyogenes Cas9 (SpCas9) has become a powerful genome editing tool, but has a limited range of recognizable protospacer adjacent motifs (PAMs) and shows off-target effects. To address these issues, we present a rational approach to optimize the xCas9 mutant derived from SpCas9 by directed evolution. Firstly, energy minimization with the Rosetta program was applied to optimize the three-dimensional structure of Cas9 to obtain the lowest energy conformation. Subsequently, combinatorial mutations were designed based on the mutations sites of xCas9 acquired during the directed evolution. Finally, optimal mutants were selected from the designed mutants by free energy ranking and subjected to experimental verification. A new mutant yCas9 (262A/324R/409N/480K/543D/694L/1219T) with multiple PAM recognition ability and low off-target effects was obtained and verified by DNA cleavage experiments. This mutant recognizes the NG, GAA and GAT PAMs and shows low off-target DNA cleavage activity guided by mismatched sgRNA, thus provides a gene editing tool with potential applications in biomedical field. Furthermore, we performed molecular dynamics simulations on the structures of SpCas9, xCas9 and yCas9 to reveal the mechanisms of their PAM recognition and off-target effects. These may provide theoretical guidance for further optimization and modification of CRISPR/Cas9 proteins.

Edição genômica como estudo da regulação da expressão do hormônio de crescimento na síndrome de Prader-Willi / Genomic editing as a study of the regulation of growth hormone expression in Prader-Willi syndrome

A síndrome de Prader-Willi (SPW) é associada a distúrbios neurológicos, comportamentais e diversas deficiências hormonais, incluindo o hormônio do crescimento (GH). Embora o tratamento de reposição do GH melhore a composição corporal, o crescimento e o quadro clínico geral, esta não é uma cura e suas bases clínicas ainda são desconhecidas na síndrome. A SPW ocorre por três mecanismos moleculares: deleção paterna da região 15q11-q13; dissomia uniparental materna 15; ou defeitos de imprinting. A linhagem celular GH3 de pituitária de rato foi utilizada por ser um modelo bem estudado de células secretoras de GH e prolactina. Utilizando o sistema CRISPR-Cas9, realizamos a deleção completa da região ortóloga da SPW de 3,2 Mb na linhagem GH3, produzindo o genótipo da síndrome in vitro, para investigar quais segmentos gênicos da SPW estão envolvidos na regulação do GH. A investigação de off-targets por sequenciamento Sanger revelou desde reparos sem alteração nucleotídica até grandes rearranjos nos flancos dos sítios-alvo dos gRNAs, inclusive com inserções não previstas de DNA exógeno. Nossos dados ressaltam a necessidade de projetar cuidadosamente as condições experimentais e caracterizar minuciosamente os materiais genéticos obtidos pelo sistema CRISPR-Cas9. A análise do DNA no flanco proximal da região da SPW em ratos demonstrou sequências que podem representar o marco inicial do silenciamento gênico por imprinting na região, assim como ocorre próximo a UBE3A em humanos na porção distal da região ortóloga. Os quatro modelos de sublinhagens SPW-Knockout gerados neste trabalho com deleções de 3,2 Mb envolvendo toda a região da SPW permitirão compreender melhor a relação entre os genes da síndrome e as vias moleculares envolvidas na regulação do GH, além da sua utilização como modelos em novos estudos sobre a SPW. O gene SNORD107 surgiu como o principal candidato a regular o GH dentro da região da SPW, podendo formar um complexo ribonucleoprotéico que exerceria função regulatória pós-transcricional na cadeia de produção do GH.

Prader-Willi syndrome (PWS) is associated with neurodevelopmental and behavioral abnormalities and numerous hormonal deficiencies, including growth hormone (GH). Although GH replacement treatment improves body composition, growth, and the overall clinical presentation, it is not a cure and its clinical basis is still unknown in the syndrome. PWS occurs by three molecular mechanisms: paternal deletion of the 15q11-q13 region; maternal uniparental disomy 15; or imprinting defects. The rat pituitary GH3 cell line is a well-studied model of GH and prolactin-secreting cells. Using the CRISPR-Cas9 system, we performed the complete deletion of the 3.2 Mb PWS orthologous region in GH3 cells, generating the syndrome genotype in vitro to investigate which PWS genes are involved in GH regulation. Off-target analysis by Sanger sequencing revealed perfect breakpoint repairs, but also large rearrangements on the flanking sites of the gRNA targets, including unexpected insertions of exogenous DNA. These data highlight the need to carefully design the experimental conditions and fully characterize the genetic materials obtained by CRISPR-Cas9. DNA analysis on the proximal flank of the PWS region in rats has shown sequences that can mark the initial borders of genomic imprinting, as it occurs close to UBE3A in humans in the distal portion of the orthologous region. The four PWS-Knockout models generated in this work with 3.2 Mb deletions involving the entire PWS region will allow a better understanding of the relationship between PWS genes and the molecular pathways involved in GH regulation and can be used as models in new PWS studies. The SNORD107 gene has emerged as the main candidate to regulate GH within the PWS region and may form a ribonucleoprotein complex with a post-transcriptional regulatory function in the GH production pathway.

Effective gene editing by high-fidelity base editor 2 in mouse zygotes

Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease-causing mutations in patients. However, problems such as mosaicism and low mutagenesis efficiency continue to pose challenges to clinical application of such approaches. Recently, a base editor (BE) system built on cytidine (C) deaminase and CRISPR/Cas9 technology was developed as an alternative method for targeted point mutagenesis in plant, yeast, and human cells. Base editors convert C in the deamination window to thymidine (T) efficiently, however, it remains unclear whether targeted base editing in mouse embryos is feasible. In this report, we generated a modified high-fidelity version of base editor 2 (HF2-BE2), and investigated its base editing efficacy in mouse embryos. We found that HF2-BE2 could convert C to T efficiently, with up to 100% biallelic mutation efficiency in mouse embryos. Unlike BE3, HF2-BE2 could convert C to T on both the target and non-target strand, expanding the editing scope of base editors. Surprisingly, we found HF2-BE2 could also deaminate C that was proximal to the gRNA-binding region. Taken together, our work demonstrates the feasibility of generating point mutations in mouse by base editing, and underscores the need to carefully optimize base editing systems in order to eliminate proximal-site deamination.