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1.
Nucleic Acids Res ; 51(18): 10075-10093, 2023 10 13.
Artículo en Inglés | MEDLINE | ID: mdl-37650635

RESUMEN

None of the existing approaches for regulating gene expression can bidirectionally and quantitatively fine-tune gene expression to desired levels. Here, on the basis of precise manipulations of the Kozak sequence, which has a remarkable influence on translation initiation, we proposed and validated a novel strategy to directly modify the upstream nucleotides of the translation initiation codon of a given gene to flexibly alter the gene translation level by using base editors and prime editors. When the three nucleotides upstream of the translation initiation codon (named KZ3, part of the Kozak sequence), which exhibits the most significant base preference of the Kozak sequence, were selected as the editing region to alter the translation levels of proteins, we confirmed that each of the 64 KZ3 variants had a different translation efficiency, but all had similar transcription levels. Using the ranked KZ3 variants with different translation efficiencies as predictors, base editor- and prime editor-mediated mutations of KZ3 in the local genome could bidirectionally and quantitatively fine-tune gene translation to the anticipated levels without affecting transcription in vitro and in vivo. Notably, this strategy can be extended to the whole Kozak sequence and applied to all protein-coding genes in all eukaryotes.


Asunto(s)
Edición Génica , Iniciación de la Cadena Peptídica Traduccional , Codón/genética , Codón Iniciador/genética , Nucleótidos/metabolismo , Biosíntesis de Proteínas , ARN Mensajero/metabolismo , Células Eucariotas
2.
BMC Biol ; 22(1): 119, 2024 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-38769511

RESUMEN

BACKGROUND: Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS: Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS: Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.


Asunto(s)
Exodesoxirribonucleasas , Edición Génica , Edición Génica/métodos , Humanos , Exodesoxirribonucleasas/genética , Exodesoxirribonucleasas/metabolismo , Sistemas CRISPR-Cas , Células HEK293 , Enzimas Reparadoras del ADN
3.
Nucleic Acids Res ; 50(9): 5384-5399, 2022 05 20.
Artículo en Inglés | MEDLINE | ID: mdl-35544322

RESUMEN

Establishing saturated mutagenesis in a specific gene through gene editing is an efficient approach for identifying the relationships between mutations and the corresponding phenotypes. CRISPR/Cas9-based sgRNA library screening often creates indel mutations with multiple nucleotides. Single base editors and dual deaminase-mediated base editors can achieve only one and two types of base substitutions, respectively. A new glycosylase base editor (CGBE) system, in which the uracil glycosylase inhibitor (UGI) is replaced with uracil-DNA glycosylase (UNG), was recently reported to efficiently induce multiple base conversions, including C-to-G, C-to-T and C-to-A. In this study, we fused a CGBE with ABE to develop a new type of dual deaminase-mediated base editing system, the AGBE system, that can simultaneously introduce 4 types of base conversions (C-to-G, C-to-T, C-to-A and A-to-G) as well as indels with a single sgRNA in mammalian cells. AGBEs can be used to establish saturated mutant populations for verification of the functions and consequences of multiple gene mutation patterns, including single-nucleotide variants (SNVs) and indels, through high-throughput screening.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Animales , Mutación INDEL , Mamíferos/genética , Mutación , Uracil-ADN Glicosidasa/genética
4.
J Virol ; 96(24): e0162622, 2022 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-36453883

RESUMEN

Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, not only causes diarrhea in piglets but also possesses the potential to infect humans. To better understand host-virus genetic dependencies and find potential therapeutic targets for PDCoV, we used a porcine single-guide RNA (sgRNA) lentivirus library to screen host factors related to PDCoV infection in LLC-PK1 cells. The solute carrier family 35 member A1 (SLC35A1), a key molecule in the sialic acid (SA) synthesis pathway, was identified as a host factor required for PDCoV infection. A knockout of SLC35A1 caused decreases in the amounts of cell surface sialic acid (SA) and viral adsorption; meanwhile, trypsin promoted the use of SA in PDCoV infection. By constructing and assessing a series of recombinant PDCoV strains with the deletion or mutation of possible critical domain or amino acid residues for SA binding in the S1 N-terminal domain, we found that S T182 might be a PDCoV SA-binding site. However, the double knockout of SLC35A1 and amino peptidase N (APN) could not block PDCoV infection completely. Additionally, we found that different swine enteric coronaviruses, including transmissible gastroenteritis coronavirus, porcine epidemic diarrhea virus, and swine acute diarrhea syndrome coronavirus, are differentially dependent on SA. Overall, our study uncovered a collection of host factors that can be exploited as drug targets against PDCoV infection and deepened our understanding of the relationship between PDCoV and SA. IMPORTANCE Identifying the host factors required for replication will be helpful to uncover the pathogenesis mechanisms and develop antivirals against the emerging coronavirus porcine deltacoronavirus (PDCoV). Herein, we performed a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 knockout screen, the results of which revealed that the solute carrier family 35 member A1 (SLC35A1) is a host factor required for PDCoV infection that acts by regulating cell surface sialic acid (SA). We also identified the T182 site in the N-terminal domain of PDCoV S1 subunit as being associated with the SA-binding site and found that trypsin promotes the use of cell surface SA by PDCoV. Furthermore, different swine enteric coronaviruses use SLC35A1 differently for infection. This is the first study to screen host factors required for PDCoV replication using a genome-wide CRISPR-Cas9 functional knockout, thereby providing clues for developing antiviral drugs against PDCoV infection.


Asunto(s)
Infecciones por Coronavirus , Interacciones Microbiota-Huesped , Proteínas de Transporte de Nucleótidos , Enfermedades de los Porcinos , Animales , Humanos , Adsorción , Coronavirus , Infecciones por Coronavirus/fisiopatología , Sistemas CRISPR-Cas , Ácido N-Acetilneuramínico/metabolismo , Proteínas de Transporte de Nucleótidos/genética , Proteínas de Transporte de Nucleótidos/metabolismo , Porcinos , Enfermedades de los Porcinos/fisiopatología , Tripsina , Interacciones Microbiota-Huesped/genética , Dominios Proteicos , Sitios de Unión
5.
J Immunol ; 205(9): 2532-2544, 2020 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-32958688

RESUMEN

The NLRP3 inflammasome is associated with a variety of human diseases, including cryopyrin-associated periodic syndrome (CAPS). CAPS is a dominantly inherited disease with NLRP3 missense mutations. Currently, most studies on the NLRP3-inflammasome have been performed with mice, but the activation patterns and the signaling pathways of the mouse NLRP3 inflammasome are not always identical with those in humans. The NLRP3 inflammasome activation in pigs is similar to that in humans. Therefore, pigs with precise NLRP3-point mutations may model human CAPS more accurately. In this study, an NLRP3 gain-of-function pig model carrying a homozygous R259W mutation was generated by combining CRISPR/Cpf1-mediated somatic cell genome editing with nuclear transfer. The newborn NLRP3 R259W homozygous piglets showed early mortality, poor growth, and spontaneous systemic inflammation symptoms, including skin lesion, joint inflammation, severe contracture, and inflammation-mediated multiorgan failure. Severe myocardial fibrosis was also observed. The tissues of inflamed skins and several organs showed significantly increased expressions of NLRP3, Caspase-1, and inflammation-associated cytokines and factors (i.e., IL-1ß, TNF-α, IL-6, and IL-17). Notably, approximately half of the homozygous piglets grew up to adulthood and even gave birth to offspring. Although the F1 heterozygous piglets showed improved survival rate and normal weight gain, 39.1% (nine out of 23) of the piglets died early and exhibited spontaneous systemic inflammation symptoms. In addition, similar to homozygotes, adult heterozygotes showed increased delayed hypersensitivity response. Thus, the NLRP3 R259W pigs are similar to human CAPS and can serve as an ideal animal model to bridge the gap between rodents and humans.


Asunto(s)
Mutación con Ganancia de Función/genética , Inflamación/genética , Proteína con Dominio Pirina 3 de la Familia NLR/genética , Porcinos/genética , Animales , Caspasa 1/genética , Síndromes Periódicos Asociados a Criopirina/genética , Citocinas/genética , Homocigoto , Humanos , Inflamasomas/genética , Masculino , Piel/metabolismo
6.
Mol Ther ; 29(3): 1001-1015, 2021 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-33221434

RESUMEN

Patients with hereditary tyrosinemia type I (HT1) present acute and irreversible liver and kidney damage during infancy. CRISPR-Cas9-mediated gene correction during infancy may provide a promising approach to treat patients with HT1. However, all previous studies were performed on adult HT1 rodent models, which cannot authentically recapitulate some symptoms of human patients. The efficacy and safety should be verified in large animals to translate precise gene therapy to clinical practice. Here, we delivered CRISPR-Cas9 and donor templates via adeno-associated virus to newborn HT1 rabbits. The lethal phenotypes could be rescued, and notably, these HT1 rabbits reached adulthood normally without 2-(2-nitro-4-trifluoromethylbenzyol)-1,3 cyclohexanedione administration and even gave birth to offspring. Adeno-associated virus (AAV)-treated HT1 rabbits displayed normal liver and kidney structures and functions. Homology-directed repair-mediated precise gene corrections and non-homologous end joining-mediated out-of-frame to in-frame corrections in the livers were observed with efficiencies of 0.90%-3.71% and 2.39%-6.35%, respectively, which appeared to be sufficient to recover liver function and decrease liver and kidney damage. This study provides useful large-animal preclinical data for rescuing hepatocyte-related monogenetic metabolic disorders with precise gene therapy.


Asunto(s)
Sistemas CRISPR-Cas , Dependovirus/genética , Edición Génica , Vectores Genéticos/administración & dosificación , Hidrolasas/genética , Tirosinemias/terapia , Animales , Animales Recién Nacidos , Reparación del ADN por Unión de Extremidades , Modelos Animales de Enfermedad , Femenino , Regulación de la Expresión Génica , Terapia Genética , Riñón/metabolismo , Hígado/metabolismo , Masculino , RNA-Seq , Conejos , Tirosinemias/genética , Tirosinemias/patología
7.
BMC Biol ; 18(1): 131, 2020 09 23.
Artículo en Inglés | MEDLINE | ID: mdl-32967664

RESUMEN

BACKGROUND: Many favorable traits of crops and livestock and human genetic diseases arise from multiple single nucleotide polymorphisms or multiple point mutations with heterogeneous base substitutions at the same locus. Current cytosine or adenine base editors can only accomplish C-to-T (G-to-A) or A-to-G (T-to-C) substitutions in the windows of target genomic sites of organisms; therefore, there is a need to develop base editors that can simultaneously achieve C-to-T and A-to-G substitutions at the targeting site. RESULTS: In this study, a novel fusion adenine and cytosine base editor (ACBE) was generated by fusing a heterodimer of TadA (ecTadAWT/*) and an activation-induced cytidine deaminase (AID) to the N- and C-terminals of Cas9 nickase (nCas9), respectively. ACBE could simultaneously induce C-to-T and A-to-G base editing at the same target site, which were verified in HEK293-EGFP reporter cell line and 45 endogenous gene loci of HEK293 cells. Moreover, the ACBE could accomplish simultaneous point mutations of C-to-T and A-to-G in primary somatic cells (mouse embryonic fibroblasts and porcine fetal fibroblasts) in an applicable efficiency. Furthermore, the spacer length of sgRNA and the length of linker could influence the dual base editing activity, which provided a direction to optimize the ACBE system. CONCLUSION: The newly developed ACBE would expand base editor toolkits and should promote the generation of animals and the gene therapy of genetic diseases with heterogeneous point mutations.


Asunto(s)
Adenina/metabolismo , Citosina/metabolismo , Embrión de Mamíferos/metabolismo , Edición Génica/instrumentación , Mutación Puntual , Animales , Feto/metabolismo , Fibroblastos/metabolismo , Células HEK293 , Humanos , Ratones , Sus scrofa
8.
Genome Res ; 27(12): 2061-2071, 2017 12.
Artículo en Inglés | MEDLINE | ID: mdl-29146772

RESUMEN

Despite being time-consuming and costly, generating genome-edited pigs holds great promise for agricultural, biomedical, and pharmaceutical applications. To further facilitate genome editing in pigs, we report here establishment of a pig line with Cre-inducible Cas9 expression that allows a variety of ex vivo genome editing in fibroblast cells including single- and multigene modifications, chromosome rearrangements, and efficient in vivo genetic modifications. As a proof of principle, we were able to simultaneously inactivate five tumor suppressor genes (TP53, PTEN, APC, BRCA1, and BRCA2) and activate one oncogene (KRAS), achieved by delivering Cre recombinase and sgRNAs, which caused rapid lung tumor development. The efficient genome editing shown here demonstrates that these pigs can serve as a powerful tool for dissecting in vivo gene functions and biological processes in a temporal manner and for streamlining the production of genome-edited pigs for disease modeling.


Asunto(s)
Animales Modificados Genéticamente , Proteínas Bacterianas/genética , Endonucleasas/genética , Edición Génica/métodos , Genoma , Porcinos Enanos/genética , Animales , Proteína 9 Asociada a CRISPR , Sistemas CRISPR-Cas/genética , Femenino , Fibroblastos/metabolismo , Reordenamiento Génico , Genes Supresores de Tumor , Humanos , Integrasas/metabolismo , Neoplasias Pulmonares/genética , Masculino , Oncogenes , Porcinos , Nucleasas de los Efectores Tipo Activadores de la Transcripción , Activación Transcripcional
9.
Hum Mol Genet ; 26(1): 184-191, 2017 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-28011715

RESUMEN

Atrichia and sparse hair phenotype cause distress to many patients. Ectodermal dysplasia-9 (ED-9) is a congenital condition characterized by hypotrichosis and nail dystrophy without other disorders, and Hoxc13 is a pathogenic gene for ED-9. However, mice carrying Hoxc13 mutation present several other serious disorders, such as skeletal defects, progressive weight loss and low viability. Mouse models cannot faithfully mimic human ED-9. In this study, we generated an ED-9 pig model via Hoxc13 gene knockout through single-stranded oligonucleotides (c.396C > A) combined with CRISPR/Cas9 and somatic cell nuclear transfer. Eight cloned piglets with three types of biallelic mutations (five piglets with Hoxc13c.396C > A/c.396C > A, two piglets with Hoxc13c.396C > A/c.396C > A + 1 and one piglet with Hoxc13Δ40/Δ40) were obtained. Hoxc13 was not expressed in pigs with all three mutation types, and the expression levels of Hoxc13-regulated genes, namely, Foxn1, Krt85 and Krt35, were decreased. The hair follicles displayed various abnormal phenotypes, such as reduced number of follicles and disarrayed hair follicle cable without normal hair all over the body. By contrast, the skin structure, skeleton phenotype, body weight gain and growth of Hoxc13 knockout pigs were apparently normal. The phenotypes of Hoxc13 mutation in pigs were similar to those in ED-9 patients. Therefore, Hoxc13 knockout pigs could be utilized as a model for ED-9 pathogenesis and as a hairless model for hair regeneration research. Moreover, the hairless pigs without other major abnormal phenotypes generated in this study could be effective models for other dermatological research because of the similarity between pig and human skins.


Asunto(s)
Modelos Animales de Enfermedad , Displasia Ectodérmica/genética , Displasia Ectodérmica/patología , Folículo Piloso/patología , Proteínas de Homeodominio/genética , Mutación/genética , Piel/patología , Animales , Secuencia de Bases , Peso Corporal , Sistemas CRISPR-Cas , Femenino , Feto/metabolismo , Feto/patología , Fibroblastos/metabolismo , Fibroblastos/patología , Folículo Piloso/metabolismo , Proteínas de Homeodominio/antagonistas & inhibidores , Proteínas de Homeodominio/metabolismo , Humanos , Masculino , Homología de Secuencia de Ácido Nucleico , Piel/metabolismo , Porcinos
10.
Cell Mol Life Sci ; 75(19): 3593-3607, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-29637228

RESUMEN

CRISPR/Cpf1 features a number of properties that are distinct from CRISPR/Cas9 and provides an excellent alternative to Cas9 for genome editing. To date, genome engineering by CRISPR/Cpf1 has been reported only in human cells and mouse embryos of mammalian systems and its efficiency is ultimately lower than that of Cas9 proteins from Streptococcus pyogenes. The application of CRISPR/Cpf1 for targeted mutagenesis in other animal models has not been successfully verified. In this study, we designed and optimized a guide RNA (gRNA) transcription system by inserting a transfer RNA precursor (pre-tRNA) sequence downstream of the gRNA for Cpf1, protecting gRNA from immediate digestion by 3'-to-5' exonucleases. Using this new gRNAtRNA system, genome editing, including indels, large fragment deletion and precise point mutation, was induced in mammalian systems, showing significantly higher efficiency than the original Cpf1-gRNA system. With this system, gene-modified rabbits and pigs were generated by embryo injection or somatic cell nuclear transfer (SCNT) with an efficiency comparable to that of the Cas9 gRNA system. These results demonstrated that this refined gRNAtRNA system can boost the targeting capability of CRISPR/Cpf1 toolkits.


Asunto(s)
Proteínas Bacterianas/genética , Sistemas CRISPR-Cas/genética , Clonación Molecular/métodos , Clonación de Organismos/métodos , Endonucleasas/genética , Edición Génica/métodos , ARN de Transferencia/genética , Animales , Animales Modificados Genéticamente , Animales Recién Nacidos , Proteínas Bacterianas/metabolismo , Células Cultivadas , Embrión de Mamíferos , Endonucleasas/metabolismo , Femenino , Feto , Genoma/genética , Células HEK293 , Células HeLa , Humanos , Masculino , Mamíferos/embriología , Mamíferos/genética , Mutagénesis , Técnicas de Transferencia Nuclear , Embarazo , ARN Guía de Kinetoplastida/genética , Conejos , Porcinos , Porcinos Enanos
12.
J Biol Chem ; 289(8): 5250-60, 2014 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-24385434

RESUMEN

Neuronal restricted progenitors (NRPs) represent a type of transitional intermediate cells that lie between multipotent neural progenitors and terminal differentiated neurons during neurogenesis. These NRPs have the ability to self-renew and differentiate into neurons, but not into glial cells, which is considered an advantage for cellular therapy of human neurodegenerative diseases. However, difficulty in the extraction of highly purified NRPs from normal nervous tissue prevents further studies and applications. In this study, we report the conversion of human fetal fibroblasts into human induced NRPs (hiNRPs) in 11 days by using just three defined factors: Sox2, c-Myc, and either Brn2 or Brn4. The hiNRPs exhibited distinct neuronal characteristics, including cell morphology, multiple neuronal marker expression, self-renewal capacity, and a genome-wide transcriptional profile. Moreover, hiNRPs were able to differentiate into various terminal neurons with functional membrane properties but not glial cells. Direct generation of hiNRPs from somatic cells will provide a new source of cells for cellular replacement therapy of human neurodegenerative diseases.


Asunto(s)
Fibroblastos/citología , Células-Madre Neurales/citología , Neuronas/citología , Animales , Diferenciación Celular , Línea Celular , Proliferación Celular , Reprogramación Celular , Perfilación de la Expresión Génica , Genoma Humano/genética , Humanos , Ratones , Células-Madre Neurales/trasplante , Trasplante de Células Madre , Factores de Transcripción/metabolismo
13.
Genome Biol ; 25(1): 108, 2024 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-38671524

RESUMEN

BACKGROUND: Prime editing enables precise base substitutions, insertions, and deletions at targeted sites without the involvement of double-strand DNA breaks or exogenous donor DNA templates. However, the large size of prime editors (PEs) hampers their delivery in vivo via adeno-associated virus (AAV) due to the viral packaging limit. Previously reported split PE versions provide a size reduction, but they require intricate engineering and potentially compromise editing efficiency. RESULTS: Herein, we present a simplified split PE named as CC-PE, created through non-covalent recruitment of reverse transcriptase to the Cas9 nickase via coiled-coil heterodimers, which are widely used in protein design due to their modularity and well-understood sequence-structure relationship. We demonstrate that the CC-PE maintains or even surpasses the efficiency of unsplit PE in installing intended edits, with no increase in the levels of undesired byproducts within tested loci amongst a variety of cell types (HEK293T, A549, HCT116, and U2OS). Furthermore, coiled-coil heterodimers are used to engineer SpCas9-NG-PE and SpRY-PE, two Cas9 variants with more flexible editing scope. Similarly, the resulting NG-CC-PE and SpRY-CC-PE also achieve equivalent or enhanced efficiency of precise editing compared to the intact PE. When the dual AAV vectors carrying CC-PE are delivered into mice to target the Pcsk9 gene in the liver, CC-PE enables highly efficient precise editing, resulting in a significant reduction of plasma low-density lipoprotein cholesterol and total cholesterol. CONCLUSIONS: Our innovative, modular system enhances flexibility, thus potentially facilitating the in vivo applicability of prime editing.


Asunto(s)
Edición Génica , Humanos , Animales , Ratones , Proteína 9 Asociada a CRISPR/metabolismo , Sistemas CRISPR-Cas , Células HEK293 , Dependovirus/genética
14.
Front Med ; 17(3): 359-387, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37434066

RESUMEN

Base editor (BE) is a gene-editing tool developed by combining the CRISPR/Cas system with an individual deaminase, enabling precise single-base substitution in DNA or RNA without generating a DNA double-strand break (DSB) or requiring donor DNA templates in living cells. Base editors offer more precise and secure genome-editing effects than other conventional artificial nuclease systems, such as CRISPR/Cas9, as the DSB induced by Cas9 will cause severe damage to the genome. Thus, base editors have important applications in the field of biomedicine, including gene function investigation, directed protein evolution, genetic lineage tracing, disease modeling, and gene therapy. Since the development of the two main base editors, cytosine base editors (CBEs) and adenine base editors (ABEs), scientists have developed more than 100 optimized base editors with improved editing efficiency, precision, specificity, targeting scope, and capacity to be delivered in vivo, greatly enhancing their application potential in biomedicine. Here, we review the recent development of base editors, summarize their applications in the biomedical field, and discuss future perspectives and challenges for therapeutic applications.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Humanos , Terapia Genética , ADN/genética
15.
Bioinform Adv ; 3(1): vbad107, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37701675

RESUMEN

Summary: Next-generation sequencing generates variants that are typically documented in variant call format (VCF) files. However, comprehensively examining variant information from VCF files can pose a significant challenge for researchers lacking bioinformatics and programming expertise. To address this issue, we introduce VCFshiny, an R package that features a user-friendly web interface enabling interactive annotation, interpretation, and visualization of variant information stored in VCF files. VCFshiny offers two annotation methods, Annovar and VariantAnnotation, to add annotations such as genes or functional impact. Annotated VCF files are deemed acceptable inputs for the purpose of summarizing and visualizing variant information. This includes the total number of variants, overlaps across sample replicates, base alterations of single nucleotides, length distributions of insertions and deletions (indels), high-frequency mutated genes, variant distribution in the genome and of genome features, variants in cancer driver genes, and cancer mutational signatures. VCFshiny serves to enhance the intelligibility of VCF files by offering an interactive web interface for analysis and visualization. Availability and implementation: The source code is available under an MIT open source license at https://github.com/123xiaochen/VCFshiny with documentation at https://123xiaochen.github.io/VCFshiny.

16.
Mol Ther Nucleic Acids ; 34: 102035, 2023 Dec 12.
Artículo en Inglés | MEDLINE | ID: mdl-37808924

RESUMEN

Cas9 protein without sgRNAs can induce genomic damage at the cellular level in vitro. However, whether the detrimental effects occur in embryos after Cas9 treatment remains unknown. Here, using pig embryos as subjects, we observed that Cas9 protein transcribed from injected Cas9 mRNA can persist until at least the blastocyst stage. Cas9 protein alone can induce genome damage in preimplantation embryos, represented by the increased number of phosphorylated histone H2AX foci on the chromatin fiber, which led to apoptosis and decreased cell number of blastocysts. In addition, single-blastocyst RNA sequencing confirmed that Cas9 protein without sgRNAs can cause changes in the blastocyst transcriptome, depressing embryo development signal pathways, such as cell cycle, metabolism, and cellular communication-related signal pathways, while activating apoptosis and necroptosis signal pathways, which together resulted in impaired preimplantation embryonic development. These results indicated that attention should be given to the detrimental effects caused by the Cas9 protein when using CRISPR-Cas9 for germline genome editing, especially for the targeted correction of human pathological mutations using germline gene therapy.

17.
Genome Biol ; 24(1): 8, 2023 01 17.
Artículo en Inglés | MEDLINE | ID: mdl-36650523

RESUMEN

BACKGROUND: CRISPR-based toolkits have dramatically increased the ease of genome and epigenome editing. SpCas9 is the most widely used nuclease. However, the difficulty of delivering SpCas9 and inability to modulate its expression in vivo hinder its widespread adoption in large animals. RESULTS: Here, to circumvent these obstacles, a doxycycline-inducible SpCas9-expressing (DIC) pig model was generated by precise knock-in of the binary tetracycline-inducible expression elements into the Rosa26 and Hipp11 loci, respectively. With this pig model, in vivo and/or in vitro genome and epigenome editing could be easily realized. On the basis of the DIC system, a convenient Cas9-based conditional knockout strategy was devised through controlling the expression of rtTA component by tissue-specific promoter, which allows the one-step generation of germline-inherited pigs enabling in vivo spatiotemporal control of gene function under simple chemical induction. To validate the feasibility of in vivo gene mutation with DIC pigs, primary and metastatic pancreatic ductal adenocarcinoma was developed by delivering a single AAV6 vector containing TP53-sgRNA, LKB1-sgRNA, and mutant human KRAS gene into the adult pancreases. CONCLUSIONS: Together, these results suggest that DIC pig resources will provide a powerful tool for conditional in vivo genome and epigenome modification for fundamental and applied research.


Asunto(s)
Sistemas CRISPR-Cas , Doxiciclina , Animales , Humanos , Doxiciclina/farmacología , Edición Génica/métodos , Genoma , Mutación , Porcinos , ARN Guía de Sistemas CRISPR-Cas/genética
18.
Sci China Life Sci ; 65(11): 2269-2286, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35596888

RESUMEN

Inducible expression systems are indispensable for precise regulation and in-depth analysis of biological process. Binary Tet-On system has been widely employed to regulate transgenic expression by doxycycline. Previous pig models with tetracycline regulatory elements were generated through random integration. This process often resulted in uncertain expression and unpredictable phenotypes, thus hindering their applications. Here, by precise knock-in of binary Tet-On 3G elements into Rosa26 and Hipp11 locus, respectively, a double knock-in reporter pig model was generated. We characterized excellent properties of this system for controllable transgenic expression both in vitro and in vivo. Two attP sites were arranged to flank the tdTomato to switch reporter gene. Single or multiple gene replacement was efficiently and faithfully achieved in fetal fibroblasts and nuclear transfer embryos. To display the flexible application of this system, we generated a pig strain with Dox-inducing hKRASG12D expression through phiC31 integrase-mediated cassette exchange. After eight months of Dox administration, squamous cell carcinoma developed in the nose, mouth, and scrotum, which indicated this pig strain could serve as an ideal large animal model to study tumorigenesis. Overall, the established pig models with controllable and switchable transgene expression system will provide a facilitating platform for transgenic and biomedical research.


Asunto(s)
Terapia Genética , Integrasas , Masculino , Animales , Porcinos , Integrasas/genética , Integrasas/metabolismo , Transgenes , Animales Modificados Genéticamente , Expresión Génica
19.
Commun Biol ; 5(1): 1163, 2022 11 02.
Artículo en Inglés | MEDLINE | ID: mdl-36323848

RESUMEN

Cas12a can process multiple sgRNAs from a single transcript of CRISPR array, conferring advantages in multiplexed base editing when incorporated into base editor systems, which is extremely helpful given that phenotypes commonly involve multiple genes or single-nucleotide variants. However, multiplexed base editing through Cas12a-derived base editors has been barely reported, mainly due to the compromised efficiencies and restricted protospacer-adjacent motif (PAM) of TTTV for wild-type Cas12a. Here, we develop Cas12a-mediated cytosine base editor (CBE) and adenine base editor (ABE) systems with elevated efficiencies and expanded targeting scope, by combining highly active deaminases with Lachnospiraceae bacterium Cas12a (LbCas12a) variants. We confirm that these CBEs and ABEs can perform efficient C-to-T and A-to-G conversions, respectively, on targets with PAMs of NTTN, TYCN, and TRTN. Notably, multiplexed base editing can be conducted using the developed CBEs and ABEs in somatic cells and embryos. These Cas12a variant-mediated base editors will serve as versatile tools for multiplexed point mutation, which is notably important in genetic improvement, disease modeling, and gene therapy.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Citosina , Adenina , Mutación Puntual
20.
Nat Commun ; 10(1): 2852, 2019 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-31253764

RESUMEN

Cytosine base editors (CBEs) enable programmable C-to-T conversion without DNA double-stranded breaks and homology-directed repair in a variety of organisms, which exhibit great potential for agricultural and biomedical applications. However, all reported cases only involved C-to-T substitution at a single targeted genomic site. Whether C-to-T substitution is effective in multiple sites/loci has not been verified in large animals. Here, by using pigs, an important animal for agriculture and biomedicine, as the subjective animal, we showed that CBEs could efficiently induce C-to-T conversions at multiple sites/loci with the combination of three genes, including DMD, TYR, and LMNA, or RAG1, RAG2, and IL2RG, simultaneously, at the embryonic and cellular levels. CBEs also could disrupt genes (pol gene of porcine endogenous retrovirus) with dozens of copies by introducing multiple premature stop codons. With the CBEs, pigs carrying single gene or multiple gene point mutations were generated through embryo injection or nuclear transfer approach.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Mutación Puntual , Porcinos/genética , Desaminasas APOBEC-1 , Animales , Secuencia de Bases , Proteína 9 Asociada a CRISPR , ADN/genética , Técnicas de Cultivo de Embriones , Embrión de Mamíferos , Genoma , Técnicas de Transferencia Nuclear/veterinaria , ARN Guía de Kinetoplastida/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo
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