hpCasMINI: An engineered hypercompact CRISPR-Cas12f system with boosted gene editing activity

Shufeng Ma, Kaitong Liao, Kechen Chen, Tong Cheng, Xiaofeng Yang, Peihan Chen, Sijie Li, Mengrao Li, Xin Zhang, Yanqun Zhang, Tao Huang, Xiaobo Wang, Lanfeng Wang, Ying Lin and Zhili Rong ()
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Shufeng Ma: Southern Medical University
Kaitong Liao: Southern Medical University
Kechen Chen: Southern Medical University
Tong Cheng: University of Chinese Academy of Sciences
Xiaofeng Yang: Southern Medical University
Peihan Chen: Southern Medical University
Sijie Li: Southern Medical University
Mengrao Li: Southern Medical University
Xin Zhang: Southern Medical University
Yanqun Zhang: Southern Medical University
Tao Huang: Southern Medical University
Xiaobo Wang: Southern Medical University
Lanfeng Wang: University of Chinese Academy of Sciences
Ying Lin: Southern Medical University
Zhili Rong: Southern Medical University

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Compact CRISPR-Cas systems have demonstrated potential for effective packaging into adeno-associated viruses (AAVs) for use in gene therapy. However, their applications are currently limited due to modest gene-editing activity. Here we introduce an engineered compact CRISPR-Cas12f (hpCasMINI, 554 aa), with hyper editing efficiency in mammalian cells via adding an α-helix structure to the N-terminus of an Un1Cas12f1 variant CasMINI (529 aa). The hpCasMINI system boosts gene activation and DNA cleavage activity with about 1.4-3.0-fold and 1.1-19.5-fold, respectively, and maintains the high specificity when compared to CasMINI. In addition, the system can activate luciferase reporter gene and endogenous Fgf21 gene in adult mouse liver, as well as construct liver tumorigenesis model via disrupting Trp53 and Pten genes and inserting oncogenic KrasG12D into the Trp53 locus. When compared to SpCas9 and LbCas12a, hpCasMINI displays higher gene activation and exhibits higher DNA cleavage specificity, although with lower activity, at the tested sites. Moreover, with a similar strategy, we engineer compact versions of hpOsCas12f1 (458 aa) from enOsCas12f1 and hpAsCas12f1 (447 aa) from AsCas12f1-HKRA, both of which display increased DNA cleavage activity, with hpAsCas12f1 also showing improved gene activation capability. Therefore, we develop activity-increased miniature hpCasMINI, hpOsCas12f1 and hpAsCas12f1 nucleases, which hold great potential for gene therapy in the future.

Date: 2025
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DOI: 10.1038/s41467-025-60124-6

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