Unveiling Off-Target Mutations in CRISPR Guide RNAs: Implications for Gene Region Specificity.

IF 3.7 4区 生物学 Q2 GENETICS & HEREDITY
Ali Mertcan Kose, Ozan Kocadagli, Cihan Taştan, Cagdas Aktan, Onur Mert Ünaldı, Elanur Güzenge, Hamza Emir Erdil
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引用次数: 0

Abstract

The revolutionary CRISPR-Cas9 technology has revolutionized genetic engineering, and it holds immense potential for therapeutic interventions. However, the presence of off-target mutations and mismatch capacity poses significant challenges to its safe and precise implementation. In this study, we explore the implications of off-target effects on critical gene regions, including exons, introns, and intergenic regions. Leveraging a benchmark dataset and using innovative data preprocessing techniques, we have put forth the advantages of categorical encoding over one-hot encoding in training machine learning classifiers. Crucially, we use latent class analysis (LCA) to uncover subclasses within the off-target range, revealing distinct patterns of gene region disruption. Our comprehensive approach not only highlights the critical role of model complexity in CRISPR applications but also offers a transformative off-target scoring procedure based on ML classifiers and LCA. By bridging the gap between traditional target-off scoring and comprehensive model analysis, our study advances the understanding of off-target effects and opens new avenues for precision genome editing in diverse biological contexts. This work represents a crucial step toward ensuring the safety and efficacy of CRISPR-based therapies, underscoring the importance of responsible genetic manipulation for future therapeutic applications.

揭示 CRISPR 引导 RNA 的脱靶突变:对基因区域特异性的影响。
革命性的 CRISPR-Cas9 技术为基因工程带来了革命性的变化,在治疗干预方面具有巨大的潜力。然而,脱靶突变和错配能力的存在对其安全、精确地实施构成了巨大挑战。在本研究中,我们探讨了脱靶效应对关键基因区域(包括外显子、内含子和基因间区域)的影响。利用基准数据集和创新的数据预处理技术,我们提出了在训练机器学习分类器时分类编码相对于单次编码的优势。最重要的是,我们利用潜类分析(LCA)发现了脱靶范围内的子类,揭示了基因区域干扰的独特模式。我们的综合方法不仅强调了模型复杂性在 CRISPR 应用中的关键作用,还提供了一种基于 ML 分类器和 LCA 的变革性脱靶评分程序。通过弥合传统的脱靶评分与综合模型分析之间的差距,我们的研究推进了对脱靶效应的理解,并为不同生物背景下的精准基因组编辑开辟了新途径。这项工作是确保基于 CRISPR 的疗法的安全性和有效性的关键一步,强调了负责任的基因操作对未来治疗应用的重要性。
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来源期刊
CRISPR Journal
CRISPR Journal Biochemistry, Genetics and Molecular Biology-Biotechnology
CiteScore
6.30
自引率
2.70%
发文量
76
期刊介绍: In recognition of this extraordinary scientific and technological era, Mary Ann Liebert, Inc., publishers recently announced the creation of The CRISPR Journal -- an international, multidisciplinary peer-reviewed journal publishing outstanding research on the myriad applications and underlying technology of CRISPR. Debuting in 2018, The CRISPR Journal will be published online and in print with flexible open access options, providing a high-profile venue for groundbreaking research, as well as lively and provocative commentary, analysis, and debate. The CRISPR Journal adds an exciting and dynamic component to the Mary Ann Liebert, Inc. portfolio, which includes GEN (Genetic Engineering & Biotechnology News) and more than 80 leading peer-reviewed journals.
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