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Article: A booming field of large animal model research.

Li, Xiao-Jiang / Lai, Liangxue

Zoological research

2024 Volume 45, Issue 2, Page(s) 311–313

MeSH term(s)	Animals ; Models, Animal
Language	English
Publishing date	2024-03-14
Publishing country	China
Document type	Editorial
ISSN	2095-8137
ISSN	2095-8137
DOI	10.24272/j.issn.2095-8137.2024.018
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Article ; Online: Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A.

Liang, Mingming / Zhang, Lichao / Lai, Liangxue / Li, Zhanjun

Cellular and molecular life sciences : CMLS

2024 Volume 81, Issue 1, Page(s) 156

Abstract: X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its ... ...

Abstract	X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X
MeSH term(s)	Humans ; Male ; Animals ; Rabbits ; Female ; X Chromosome Inactivation/genetics ; RNA, Long Noncoding/genetics ; Chromosomes, Human, X ; X Chromosome/genetics ; Exons/genetics
Chemical Substances	RNA, Long Noncoding
Language	English
Publishing date	2024-03-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-024-05151-0
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Zs.A 195: Show issues

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Article ; Online: Base editors: development and applications in biomedicine.

Liang, Yanhui / Chen, Fangbing / Wang, Kepin / Lai, Liangxue

Frontiers of medicine

2023 Volume 17, Issue 3, Page(s) 359–387

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Humans ; Gene Editing ; CRISPR-Cas Systems ; Genetic Therapy ; DNA/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-07-12
Publishing country	China
Document type	Journal Article ; Review
ZDB-ID	2617113-2
ISSN	2095-0225 ; 2095-0217
ISSN (online)	2095-0225
ISSN	2095-0217
DOI	10.1007/s11684-023-1013-y
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Article: Genome-edited rabbits: Unleashing the potential of a promising experimental animal model across diverse diseases.

Han, Yang / Zhou, Jiale / Zhang, Renquan / Liang, Yuru / Lai, Liangxue / Li, Zhanjun

Zoological research

2024 Volume 45, Issue 2, Page(s) 253–262

Abstract: Animal models are extensively used in all aspects of biomedical research, with substantial contributions to our understanding of diseases, the development of pharmaceuticals, and the exploration of gene functions. The field of genome modification in ... ...

Abstract	Animal models are extensively used in all aspects of biomedical research, with substantial contributions to our understanding of diseases, the development of pharmaceuticals, and the exploration of gene functions. The field of genome modification in rabbits has progressed slowly. However, recent advancements, particularly in CRISPR/Cas9-related technologies, have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases, including cardiovascular disorders, immunodeficiencies, aging-related ailments, neurological diseases, and ophthalmic pathologies. These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice. This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine, underscoring their impact and future potential in translational medicine.
MeSH term(s)	Humans ; Rabbits ; Animals ; Mice ; CRISPR-Cas Systems ; Veterinary Drugs ; Gene Editing/veterinary ; Models, Animal ; Biomedical Research
Chemical Substances	Veterinary Drugs
Language	English
Publishing date	2024-01-29
Publishing country	China
Document type	Journal Article ; Review
ISSN	2095-8137
ISSN	2095-8137
DOI	10.24272/j.issn.2095-8137.2023.201
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Article ; Online: Inhibition of base editors with anti-deaminases derived from viruses

Zhiquan Liu / Siyu Chen / Liangxue Lai / Zhanjun Li

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 11

Abstract: Anti-deaminases can inhibit APOBEC3, a component of cytosine base editors. Here Zhanjun Li and colleagues repurposed anti-deaminase proteins derived from viruses to inhibit base editors for use in efficient regulation of base editors’ activity in gene ... ...

Abstract	Anti-deaminases can inhibit APOBEC3, a component of cytosine base editors. Here Zhanjun Li and colleagues repurposed anti-deaminase proteins derived from viruses to inhibit base editors for use in efficient regulation of base editors’ activity in gene modification and therapeutic applications.
Keywords	Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Efficient C-to-G Base Editing with Improved Target Compatibility Using Engineered Deaminase-nCas9 Fusions.

Chen, Siyu / Liu, Zhiquan / Lai, Liangxue / Li, Zhanjun

The CRISPR journal

2022 Volume 5, Issue 3, Page(s) 389–396

Abstract: CRISPR-guided DNA base editors (BEs) are potent genome editing tools in biotechnology and medicine. However, conventional cytosine and adenine BEs can only induce base transitions (C-to-T and A-to-G) and cannot induce base transversions. Recently, ... ...

Abstract	CRISPR-guided DNA base editors (BEs) are potent genome editing tools in biotechnology and medicine. However, conventional cytosine and adenine BEs can only induce base transitions (C-to-T and A-to-G) and cannot induce base transversions. Recently, several C-to-G base editors (CGBEs) were generated and applied in human cells. By comparing them, we found that engineered deaminases rather than additional base excision repair proteins significantly improved the C-to-G efficiency. In addition, significant increase in C-to-G transversions in the GC context were determined by using rationally engineered eAID deaminase. The genome-targeting scope of CGBEs were further expanded by using SpRY Cas9 variant, which then successfully induced stop codon (TAC to TAG) to disrupt
MeSH term(s)	Adenine ; Animals ; CRISPR-Cas Systems/genetics ; Cytosine ; Gene Editing ; Genome ; Mice
Chemical Substances	Cytosine (8J337D1HZY) ; Adenine (JAC85A2161)
Language	English
Publishing date	2022-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3017891-5
ISSN	2573-1602 ; 2573-1599
ISSN (online)	2573-1602
ISSN	2573-1599
DOI	10.1089/crispr.2021.0124
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Zs.A 7195: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Inhibition of base editors with anti-deaminases derived from viruses.

Liu, Zhiquan / Chen, Siyu / Lai, Liangxue / Li, Zhanjun

Nature communications

2022 Volume 13, Issue 1, Page(s) 597

Abstract: Cytosine base editors (CBEs), combining cytidine deaminases with the Cas9 nickase (nCas9), enable targeted C-to-T conversions in genomic DNA and are powerful genome-editing tools used in biotechnology and medicine. However, the overexpression of cytidine ...

Abstract	Cytosine base editors (CBEs), combining cytidine deaminases with the Cas9 nickase (nCas9), enable targeted C-to-T conversions in genomic DNA and are powerful genome-editing tools used in biotechnology and medicine. However, the overexpression of cytidine deaminases in vivo leads to unexpected potential safety risks, such as Cas9-independent off-target effects. This risk makes the development of deaminase off switches for modulating CBE activity an urgent need. Here, we report the repurpose of four virus-derived anti-deaminases (Ades) that efficiently inhibit APOBEC3 deaminase-CBEs. We demonstrate that they antagonize CBEs by inhibiting the APOBEC3 catalytic domain, relocating the deaminases to the extranuclear region or degrading the whole CBE complex. By rationally engineering the deaminase domain, other frequently used base editors, such as CGBE, A&CBE, A&CGBE, rA1-CBE and ABE8e, can be moderately inhibited by Ades, expanding the scope of their applications. As a proof of concept, the Ades in this study dramatically decrease both Cas9-dependent and Cas9-independent off-target effects of CBEs better than traditional anti-CRISPRs (Acrs). Finally, we report the creation of a cell type-specific CBE-ON switch based on a microRNA-responsive Ade vector, showing its practicality. In summary, these natural deaminase-specific Ades are tools that can be used to regulate the genome-engineering functions of BEs.
MeSH term(s)	APOBEC Deaminases ; CRISPR-Cas Systems ; Cytidine Deaminase/genetics ; Cytidine Deaminase/metabolism ; Cytosine ; DNA ; Deoxyribonuclease I ; Gene Editing ; Genetic Therapy ; HEK293 Cells ; Humans ; Viruses/genetics ; Viruses/metabolism
Chemical Substances	Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; Deoxyribonuclease I (EC 3.1.21.1) ; APOBEC Deaminases (EC 3.5.4.5) ; APOBEC3 proteins, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5)
Language	English
Publishing date	2022-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28300-0
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Article ; Online: Targeted mutagenesis in mice via an engineered AsCas12f1 system.

Fan, Peng / Wang, Hejun / Zhao, Feiyu / Zhang, Tao / Li, Jinze / Sun, Xiaodi / Yu, Yongduo / Xiong, Haoyang / Lai, Liangxue / Sui, Tingting

Cellular and molecular life sciences : CMLS

2024 Volume 81, Issue 1, Page(s) 63

Abstract: SpCas9 and AsCas12a are widely utilized as genome editing tools in human cells, but their applications are largely limited by their bulky size. Recently, AsCas12f1 protein, with a small size (422 amino acids), has been demonstrated to be capable of ... ...

Abstract	SpCas9 and AsCas12a are widely utilized as genome editing tools in human cells, but their applications are largely limited by their bulky size. Recently, AsCas12f1 protein, with a small size (422 amino acids), has been demonstrated to be capable of cleaving double-stranded DNA protospacer adjacent motif (PAM). However, low editing efficiency and large differences in activity against different genomic loci have been a limitation in its application. Here, we show that engineered AsCas12f1 sgRNA has significantly improved the editing efficiency in human cells and mouse embryos. Moreover, we successfully generated three stable mouse mutant disease models using the engineered CRISPR-AsCas12f1 system in this study. Collectively, our work uncovers the engineered AsCas12f1 system expands mini CRISPR toolbox, providing a remarkable promise for therapeutic applications.
MeSH term(s)	Mice ; Animals ; Humans ; CRISPR-Cas Systems/genetics ; CRISPR-Associated Protein 9/genetics ; CRISPR-Associated Protein 9/metabolism ; RNA, Guide, CRISPR-Cas Systems ; Streptococcus pyogenes ; Gene Editing ; Mutagenesis
Chemical Substances	CRISPR-Associated Protein 9 (EC 3.1.-) ; RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2024-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-05100-3
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Zs.A 195: Show issues

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Article ; Online: Programmable RNA 5-methylcytosine (m5C) modification of cellular RNAs by dCasRx conjugated methyltransferase and demethylase.

Zhang, Tao / Zhao, Feiyu / Li, Jinze / Sun, Xiaodi / Zhang, Xiyun / Wang, Hejun / Fan, Peng / Lai, Liangxue / Li, Zhanjun / Sui, Tingting

Nucleic acids research

2024 Volume 52, Issue 6, Page(s) 2776–2791

Abstract: 5-Methylcytosine (m5C), an abundant RNA modification, plays a crucial role in regulating RNA fate and gene expression. While recent progress has been made in understanding the biological roles of m5C, the inability to introduce m5C at specific sites ... ...

Abstract	5-Methylcytosine (m5C), an abundant RNA modification, plays a crucial role in regulating RNA fate and gene expression. While recent progress has been made in understanding the biological roles of m5C, the inability to introduce m5C at specific sites within transcripts has hindered efforts to elucidate direct links between specific m5C and phenotypic outcomes. Here, we developed a CRISPR-Cas13d-based tool, named reengineered m5C modification system (termed 'RCMS'), for targeted m5C methylation and demethylation in specific transcripts. The RCMS editors consist of a nuclear-localized dCasRx conjugated to either a methyltransferase, NSUN2/NSUN6, or a demethylase, the catalytic domain of mouse Tet2 (ten-eleven translocation 2), enabling the manipulation of methylation events at precise m5C sites. We demonstrate that the RCMS editors can direct site-specific m5C incorporation and demethylation. Furthermore, we confirm their effectiveness in modulating m5C levels within transfer RNAs and their ability to induce changes in transcript abundance and cell proliferation through m5C-mediated mechanisms. These findings collectively establish RCMS editors as a focused epitranscriptome engineering tool, facilitating the identification of individual m5C alterations and their consequential effects.
MeSH term(s)	Animals ; Mice ; 5-Methylcytosine/metabolism ; Methylation ; Methyltransferases/genetics ; Methyltransferases/metabolism ; RNA, Transfer/metabolism ; Genetic Techniques ; CRISPR-Cas Systems ; Humans ; RNA Editing
Chemical Substances	5-Methylcytosine (6R795CQT4H) ; Methyltransferases (EC 2.1.1.-) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae110
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Article: Highly efficient A-to-G base editing by ABE8.17 in rabbits.

Zhao, Ding / Qian, Yuqiang / Li, Jinze / Li, Zhanjun / Lai, Liangxue

Molecular therapy. Nucleic acids

2022 Volume 27, Page(s) 1156–1163

Abstract: Adenine base editors (ABEs), composed of an evolved adenine deaminase fused to the Cas9 nickase, enable efficient and precise A-to-G conversion in various organisms. However, the base editing of some challenging loci with the ABE7.10 system in rabbits ... ...

Abstract	Adenine base editors (ABEs), composed of an evolved adenine deaminase fused to the Cas9 nickase, enable efficient and precise A-to-G conversion in various organisms. However, the base editing of some challenging loci with the ABE7.10 system in rabbits was inefficient in our previous study. Here, we show that ABE8.17 and SpRY-ABE8.17 can efficiently induce base editing in mouse and rabbit embryos. In addition, this strategy can be used to precisely mimic clinical point mutations in rabbits. Furthermore, by eliminating the linker in ABE8.17, we created ABE8.17-NL, which achieved efficient base editing within a narrowed window (2-4 nts) in human HEK293FT cells. Collectively, these findings show that ABE8.17 systems can efficiently induce efficient A-to-G base editing at desired sites and that the ABE7.10 system is inefficient, thus providing an efficient way to generate ideal disease models in rabbits.
Language	English
Publishing date	2022-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2022.01.019
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