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1. Integrating Biomaterials and Genome Editing Approaches to Advance Biomedical Science

   https://doi.org/10.1146/annurev-bioeng-122019-121602  

   Abdeen, Amr A.; Cosgrove, Brian D.; Gersbach, Charles A.; Saha, Krishanu (July 2021, Annual Review of Biomedical Engineering)

   null (Ed.)

   The recent discovery and subsequent development of the CRISPR–Cas9 (clustered regularly interspaced short palindromic repeat–CRISPR-associated protein 9) platform as a precise genome editing tool have transformed biomedicine. As these CRISPR-based tools have matured, multiple stages of the gene editing process and the bioengineering of human cells and tissues have advanced. Here, we highlight recent intersections in the development of biomaterials and genome editing technologies. These intersections include the delivery of macromolecules, where biomaterial platforms have been harnessed to enable nonviral delivery of genome engineering tools to cells and tissues in vivo. Further, engineering native-like biomaterial platforms for cell culture facilitates complex modeling of human development and disease when combined with genome engineering tools. Deeper integration of biomaterial platforms in these fields could play a significant role in enabling new breakthroughs in the application of gene editing for the treatment of human disease. 

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2. Exploring Advanced CRISPR Delivery Technologies for Therapeutic Genome Editing

   https://doi.org/10.1002/smsc.202400192  

   Rostami, Neda; Gomari, Mohammad Mahmoudi; Choupani, Edris; Abkhiz, Shadi; Fadaie, Mahmood; Eslami, Seyed Sadegh; Mahmoudi, Zahra; Zhang, Yapei; Puri, Madhu; Monfared, Fatemeh Nafe; et al (July 2024, Small Science)

   The genetic material within cells plays a pivotal role in shaping the structure and function of living organisms. Manipulating an organism's genome to correct inherited abnormalities or introduce new traits holds great promise. Genetic engineering techniques offers promising pathways for precisely altering cellular genetics. Among these methodologies, clustered regularly interspaced short palindromic repeat (CRISPR), honored with the 2020 Nobel Prize in Chemistry, has garnered significant attention for its precision in editing genomes. However, the CRISPR system faces challenges when applied in vivo, including low delivery efficiency, off‐target effects, and instability. To address these challenges, innovative technologies for targeted and precise delivery of CRISPR have emerged. Engineered carrier platforms represent a substantial advancement, improving stability, precision, and reducing the side effects associated with genome editing. These platforms facilitate efficient local and systemic genome engineering of various tissues and cells, including immune cells. This review explores recent advances, benefits, and challenges of CRISPR‐based genome editing delivery. It examines various carriers including nanocarriers (polymeric, lipid‐derived, metallic, and bionanoparticles), viral particles, virus‐like particles, and exosomes, providing insights into their clinical utility and future prospects. 

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3. Reversible RNA acylation for control of CRISPR–Cas9 gene editing

   https://doi.org/10.1039/C9SC03639C  

   Habibian, Maryam; McKinlay, Colin; Blake, Timothy R.; Kietrys, Anna M.; Waymouth, Robert M.; Wender, Paul A.; Kool, Eric T. (January 2020, Chemical Science)

   null (Ed.)

   We report the development of post-transcriptional chemical methods that enable control over CRISPR–Cas9 gene editing activity both in in vitro assays and in living cells. We show that an azide-substituted acyl imidazole reagent (NAI-N 3 ) efficiently acylates CRISPR single guide RNAs (sgRNAs) in 20 minutes in buffer. Poly-acylated (“cloaked”) sgRNA was completely inactive in DNA cleavage with Cas9 in vitro , and activity was quantitatively restored after phosphine treatment. Delivery of cloaked sgRNA and Cas9 mRNA into HeLa cells was enabled by the use of charge-altering releasable transporters (CARTs), which outperformed commercial transfection reagents in transfecting sgRNA co-complexed with Cas9 encoding functional mRNA. Genomic DNA cleavage in the cells by CRISPR–Cas9 was efficiently restored after treatment with phosphine to remove the blocking acyl groups. Our results highlight the utility of reversible RNA acylation as a novel method for temporal control of genome-editing function. 

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4. Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing

   https://doi.org/10.1007/s42994-019-00014-w  

   Hsieh-Feng, Vicki; Yang, Yinong (January 2020, aBIOTECH)

   The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein system (CRISPR/Cas) has recently become the most powerful tool available for genome engineering in various organisms. With efficient and proper expression of multiple guide RNAs (gRNAs), the CRISPR/Cas system is particularly suitable for multiplex genome editing. During the past several years, different CRISPR/Cas expression strategies, such as two-component transcriptional unit, single transcriptional unit, and bidirectional promoter systems, have been developed to efficiently express gRNAs as well as Cas nucleases. Significant progress has been made to optimize gRNA production using different types of promoters and RNA processing strategies such as ribozymes, endogenous RNases, and exogenous endoribonuclease (Csy4). Besides being constitutively and ubiquitously expressed, inducible and spa- tiotemporal regulations of gRNA expression have been demonstrated using inducible, tissue-specific, and/or synthetic promoters for specific research purposes. Most recently, the emergence of CRISPR/Cas ribonucleoprotein delivery methods, such as engineered nanoparticles, further revolutionized trans- gene-free and multiplex genome editing. In this review, we discuss current strategies and future per- spectives for efficient expression and engineering of gRNAs with a goal to facilitate CRISPR/Cas-based multiplex genome editing. 

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5. dCas9-based gene editing for cleavage-free genomic knock-in of long sequences

   https://doi.org/10.1038/s41556-021-00836-1  

   Wang, Chengkun; Qu, Yuanhao; Cheng, Jason K.; Hughes, Nicholas W.; Zhang, Qianhe; Wang, Mengdi; Cong, Le (February 2022, Nature Cell Biology)

   Abstract Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. 

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