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Special Issue "CRISPR-Cas Systems and Genome Editing"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 31 October 2023 | Viewed by 5333

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Special Issue Editor

Dr. Dmitry Karpov

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Guest Editor

Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia
Interests: CRISPR/Cas; genome editing; yeast; intracellular proteolysis; transcription regulation; Bacilli; stress responses

Special Issue Information

Dear Colleagues,

Almost everyone has heard of CRISPR/Cas systems. The use of CRISPR/Cas systems as RNA-programmable site-directed nucleases has given a powerful impulse to the further development of genome editing technology. Moreover, numerous modifications of CRISPR/Cas systems have enabled the development of principally new methods for genome engineering. New molecular tools have also become widespread in other areas of science, biotechnology and biomedicine. The emergence of such versatile, relatively easy-to-use and effective molecular tools has increased human hope for effective treatment of hereditary, bacterial, or viral diseases. However, CRISPR/Cas systems have a number of drawbacks that limit their application in therapeutic approaches. Thus, research to find new genome editors, modify existing genome editing technologies, and study the universe of defense mechanisms of prokaryotes may lead to the development of fundamentally new approaches to genome editing. This special issue aims to cover all areas of both basic research on CRISPR/Cas and other genome editing systems and their applications in basic science, biotechnology, and biomedicine. It welcomes original research, theoretical articles, reviews, and communications in which CRISPR/Cas or other genome editing technologies are a major topic or tool for mechanistic molecular research. This includes, but is not limited to, methodological advances in genome editing technologies and their applications to the study and treatment of hereditary, bacterial or viral human diseases, the development of new microbial producents, cultivated plant lines and fungi.

Please note that, for IJMS’paper, theoretical studies should offer new insights into the understanding of experimental results or suggest new experimentally testable hypotheses.

Dr. Dmitry Karpov
Guest Editor

Manuscript Submission Information

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Keywords

prokaryotic defense systems with genome editing potential (CRISPR/Cas, bacterial argonauts, etc.)
development or improvement of genome editing tools
genome editing technologies in the generation and study of cellular, multicellular or animal models of hereditary, bacterial, or viral human diseases
CRISPR/Cas systems in the therapy of human diseases
genome editing to probe biotechnological processes and improve microbial producents, cultivated plants, and fungi

Published Papers (4 papers)

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Research

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Open AccessArticle

Complete and Prolonged Inhibition of Herpes Simplex Virus Type 1 Infection In Vitro by CRISPR/Cas9 and CRISPR/CasX Systems

Dmitry S. Karpov

Natalia A. Demidova

Kirill A. Kulagin

Anastasija I. Shuvalova

Maxim A. Kovalev

Ruslan A. Simonov

Vadim L. Karpov

Anastasiya V. Snezhkina

Anna V. Kudryavtseva

Regina R. Klimova

and

Alla A. Kushch

Int. J. Mol. Sci. 2022, 23(23), 14847; https://doi.org/10.3390/ijms232314847 - 27 Nov 2022

Cited by 1 | Viewed by 2527

Abstract

Almost all people become infected with herpes viruses, including herpes simplex virus type 1 (HSV-1), during their lifetime. Typically, these viruses persist in a latent form that is resistant to all available antiviral medications. Under certain conditions, such as immunosuppression, the latent forms reactivate and cause disease. Moreover, strains of herpesviruses that are drug-resistant have rapidly emerged. Therefore, it is important to develop alternative methods capable of eradicating herpesvirus infections. One promising direction is the development of CRISPR/Cas systems for the therapy of herpesvirus infections. We aimed to design a CRISPR/Cas system for relatively effective long-term and safe control of HSV-1 infection. Here, we show that plasmids encoding the CRISPR/Cas9 system from Streptococcus pyogenes with a single sgRNA targeting the UL30 gene can completely suppress HSV-1 infection of the Vero cell line within 6 days and provide substantial protection within 9 days. For the first time, we show that CRISPR/CasX from Deltaproteobacteria with a single guide RNA against UL30 almost completely suppresses HSV-1 infection of the Vero cell line for 3 days and provides substantial protection for 6 days. We also found that the Cas9 protein without sgRNAs attenuates HSV-1 infection. Our results show that the developed CRISPR/Cas systems are promising therapeutic approaches to control HSV-1 infections. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing)

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Review

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Open AccessReview

Evolution of CRISPR/Cas Systems for Precise Genome Editing

Magdalena Hryhorowicz

Daniel Lipiński

and

Joanna Zeyland

Int. J. Mol. Sci. 2023, 24(18), 14233; https://doi.org/10.3390/ijms241814233 - 18 Sep 2023

Viewed by 496

Abstract

The bacteria-derived CRISPR/Cas (an acronym for regularly interspaced short palindromic repeats/CRISPR-associated protein) system is currently the most widely used, versatile, and convenient tool for genome engineering. CRISPR/Cas-based technologies have been applied to disease modeling, gene therapies, transcriptional modulation, and diagnostics. Nevertheless, some challenges remain, such as the risk of immunological reactions or off-target effects. To overcome these problems, many new methods and CRISPR/Cas-based tools have been developed. In this review, we describe the current classification of CRISPR systems and new precise genome-editing technologies, summarize the latest applications of this technique in several fields of research, and, finally, discuss CRISPR/Cas system limitations, ethical issues, and challenges. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing)

Open AccessReview

Evidence-Based Guide to Using Artificial Introns for Tissue-Specific Knockout in Mice

Elena McBeath

Keigi Fujiwara

and

Marie-Claude Hofmann

Int. J. Mol. Sci. 2023, 24(12), 10258; https://doi.org/10.3390/ijms241210258 - 17 Jun 2023

Viewed by 732

Abstract

Up until recently, methods for generating floxed mice either conventionally or by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 (CRISPR-associated protein 9) editing have been technically challenging, expensive and error-prone, or time-consuming. To circumvent these issues, several labs have started successfully using a small artificial intron to conditionally knockout (KO) a gene of interest in mice. However, many other labs are having difficulty getting the technique to work. The key problem appears to be either a failure in achieving correct splicing after the introduction of the artificial intron into the gene or, just as crucial, insufficient functional KO of the gene’s protein after Cre-induced removal of the intron’s branchpoint. Presented here is a guide on how to choose an appropriate exon and where to place the recombinase-regulated artificial intron (rAI) in that exon to prevent disrupting normal gene splicing while maximizing mRNA degradation after recombinase treatment. The reasoning behind each step in the guide is also discussed. Following these recommendations should increase the success rate of this easy, new, and alternative technique for producing tissue-specific KO mice. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing)

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Open AccessReview

Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies

Kiriaki Paschoudi

Evangelia Yannaki

and

Nikoletta Psatha

Int. J. Mol. Sci. 2023, 24(11), 9527; https://doi.org/10.3390/ijms24119527 - 31 May 2023

Cited by 1 | Viewed by 920

Abstract

Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing)

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Special Issue "CRISPR-Cas Systems and Genome Editing"

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