scholarly journals CRISPR-mediated base editing in mice using cytosine deaminase base editor 4

2021 ◽  
Author(s):  
Salah Adlat ◽  
Farooq Hayel ◽  
Ping Yang ◽  
Yang Chen ◽  
Zin Mar Oo ◽  
...  
Keyword(s):  
Cytosine Deaminase ◽  
Base Editing

scholarly journals CRISPR-dCas9 Mediated Cytosine Deaminase Base Editing in Bacillus subtilis

2020 ◽  
Vol 9 (7) ◽  
pp. 1781-1789
Author(s):  
Sili Yu ◽  
Marcus A. Price ◽  
Yu Wang ◽  
Yang Liu ◽  
Yanmei Guo ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Cytosine Deaminase ◽  
Base Editing

scholarly journals Precise and programmable C:G to G:C base editing in genomic DNA

2020 ◽  
Author(s):  
Liwei Chen ◽  
Jung Eun Park ◽  
Peter Paa ◽  
Priscilla D. Rajakumar ◽  
Yi Ting Chew ◽  
...  
Keyword(s):  
Therapeutic Potential ◽  
Excision Repair ◽  
Genetic Diseases ◽  
Cytosine Deaminase ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Base Editing ◽  
Guide Rnas ◽  
Base Excision ◽  
Nucleotide Resolution

AbstractMany genetic diseases are caused by single-nucleotide polymorphisms (SNPs). Base editors can correct SNPs at single-nucleotide resolution, but until recently, only allowed for C:G to T:A and A:T to G:C transition edits, addressing four out of twelve possible DNA base substitutions. Here we developed a novel class of C:G to G:C Base Editors (CGBEs) to create single-base genomic transversions in human cells. Our CGBEs consist of a nickase CRISPR-Cas9 (nCas9) fused to a cytosine deaminase and base excision repair (BER) proteins. Characterization of >30 CGBE candidates and 27 guide RNAs (gRNAs) revealed that CGBEs predominantly perform C:G to G:C editing (up to 90% purity), with rAPOBEC-nCas9-rXRCC1 being the most efficient (mean C:G to G:C edits at 15% and up to 37%). CGBEs target cytosine in WCW, ACC or GCT sequence contexts and within a precise two-nucleotide window of the target protospacer. We further targeted genes linked to dyslipidemia, hypertrophic cardiomyopathy, and deafness, showing the therapeutic potential of CGBE in interrogating and correcting human genetic diseases.

scholarly journals High-efficiency plastome base-editing in rice with TAL cytosine deaminase

2021 ◽  
Author(s):  
Riqing Li ◽  
Si Nian Char ◽  
Bo Liu ◽  
Hua Liu ◽  
Xianran Li ◽  
...  
Keyword(s):  
High Efficiency ◽  
Cytosine Deaminase ◽  
Base Editing

A split cytosine deaminase architecture enables robust inducible base editing

2021 ◽  
Vol 35 (12) ◽  
Author(s):  
Jie Long ◽  
Nan Liu ◽  
Wenling Tang ◽  
Lifang Xie ◽  
Fengming Qin ◽  
...  
Keyword(s):  
Cytosine Deaminase ◽  
Base Editing

Microbial enzymes used in prodrug activation for cancer therapy: Insights and future perspectives

2020 ◽  
Vol 21 ◽  
Author(s):  
Rakhi Dhankhar ◽  
Anubhuti Kawatra ◽  
Aparajita Mohanty ◽  
Pooja Gulati
Keyword(s):  
Purine Nucleoside Phosphorylase ◽  
Cytosine Deaminase ◽  
Therapeutic Index ◽  
Enzyme Prodrug Therapy ◽  
Prodrug Activation ◽  
Microbial Enzymes ◽  
High Productivity ◽  
Delivery Vector ◽  
Exogenous Enzymes ◽  
Activation Therapy

Abstract:: Enzyme prodrug therapy has gained momentum in the recent years due to their ability to improve therapeutic index (benefits versus toxic side-effects) and efficacy of chemotherapy in cancer treatment. Inactive prodrugs used in this system are converted into active anti-cancerous drugs by enzymes, specifically within the tumor cells. This therapy involves three components namely prodrug, enzyme and gene delivery vector. Past reports have clearly indicated that the choice of enzyme used, is the major determinant for the success of this therapy. Generally, enzymes from non-human sources are employed to avoid off-target toxicity. Exogenous enzymes also give a better control to the clinician regarding the calibration of treatment by site-specific initiation. Amongst these exo-enzymes, microbial enzymes are preferred due to their high productivity, stability and ease of manipulation. The present review focuses on the commonly used microbial enzymes particularly cytosine deaminase, nitroreductase, carboxypeptidase, purine nucleoside phosphorylase in prodrug activation therapy. Various aspects viz. source of the enzymes, types of cancer targeted, mode of action and efficacy of the enzyme/prodrug system, efficient vectors used and recent research developments of each of these enzymes are comprehensively elaborated. Further, the results of the clinical trials and various strategies to improve their clinical applicability are also discussed.

scholarly journals Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 283
Author(s):  
Eyal Seroussi
Keyword(s):  
Copy Number ◽  
Sanger Sequencing ◽  
Cytosine Methylation ◽  
Direct Sequencing ◽  
Information Source ◽  
Gene Copy Number ◽  
Cost Effective ◽  
Gene Copy ◽  
Base Editing ◽  
Recent Developments

Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.

scholarly journals Lentiviral Vectors for Delivery of Gene-Editing Systems Based on CRISPR/Cas: Current State and Perspectives

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1288
Author(s):  
Wendy Dong ◽  
Boris Kantor
Keyword(s):  
Large Scale ◽  
Lentiviral Vector ◽  
Clinical Applications ◽  
Scale Production ◽  
Base Editing ◽  
Epigenome Editing ◽  
Vector Systems ◽  
Dividing Cells

CRISPR/Cas technology has revolutionized the fields of the genome- and epigenome-editing by supplying unparalleled control over genomic sequences and expression. Lentiviral vector (LV) systems are one of the main delivery vehicles for the CRISPR/Cas systems due to (i) its ability to carry bulky and complex transgenes and (ii) sustain robust and long-term expression in a broad range of dividing and non-dividing cells in vitro and in vivo. It is thus reasonable that substantial effort has been allocated towards the development of the improved and optimized LV systems for effective and accurate gene-to-cell transfer of CRISPR/Cas tools. The main effort on that end has been put towards the improvement and optimization of the vector’s expression, development of integrase-deficient lentiviral vector (IDLV), aiming to minimize the risk of oncogenicity, toxicity, and pathogenicity, and enhancing manufacturing protocols for clinical applications required large-scale production. In this review, we will devote attention to (i) the basic biology of lentiviruses, and (ii) recent advances in the development of safer and more efficient CRISPR/Cas vector systems towards their use in preclinical and clinical applications. In addition, we will discuss in detail the recent progress in the repurposing of CRISPR/Cas systems related to base-editing and prime-editing applications.

Advances in base editing with an emphasis on an AAV-based strategy

Methods ◽  
2021 ◽  
Author(s):  
Jiajie Kuang ◽  
Qinghua Lyu ◽  
Jiao Wang ◽  
Yubo Cui ◽  
Jun Zhao
Keyword(s):  
Base Editing
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