Researchers from Japan have established a new in vivo genome-editing system, CRISPR–Cas3, as a promising therapeutic approach for ATTR
CRISPR–Cas9-based therapies are widely investigated for their clinical applications. However, there are limitations associated with the strategy, including off-target DNA editing. A group of researchers from Japan has explored a novel strategy involving CRISPR–Cas3 and investigated its potential using a mouse model of transthyretin amyloidosis (ATTR). The results highlight its potential as an efficient genome-editing system. The technology can be developed as a therapeutic strategy for treating ATTR and other genetic disorders.
Genetic disorders occur due to alterations in the primary genetic material, deoxyribonucleic acid (DNA), of an organism. Transthyretin amyloidosis (ATTR) is a progressive disorder involving amyloid deposits of misfolded transthyretin (TTR) proteins. The deposits, mainly affecting the heart and the nerves, can lead to symptoms like heart failure and neuropathy. While one of its two major forms is associated with age, the other one is hereditary, resulting from destabilizing mutations in the TTR gene. The therapeutic efficacy of suppressing TTR production has been clearly demonstrated. Although ribonucleic acid (RNA) interference-based drugs can reduce TTR production, they require long-term administration and do not provide a curative treatment.
In recent times, several gene-editing strategies are being utilized to precisely alter the DNA, correcting the mutations or deleting the harmful genetic sequences. These approaches offer enhanced precision and can completely cure genetic disorders. Clustered regularly interspaced short palindromic repeats (CRISPR) refer to the small fragments of viral DNA that are stored by the bacteria as a part of their defense mechanism. CRISPR–Cas9 is a revolutionary gene-editing tool, adapted from this bacterial immune system, that has been widely explored for its clinical applications in recent times.
While the CRISPR–Cas9 shows promising results in developing revolutionary therapies, it has certain limitations, including unintended DNA cuts. Recently, a group of scientists from Japan, led by Professor Tomoji Mashimo and Dr. Saeko Ishida from the Institute of Medical Science, The University of Tokyo, Japan, evaluated the efficacy of the CRISPR–Cas3 system in safely achieving a permanent reduction of TTR production through genome editing of the TTR gene. “Genome editing holds the unique potential to correct the inherited disease-associated genetic abnormalities. We wanted to see if the CRISPR–Cas3 system can be developed as an efficient therapeutic genome-editing tool,” mentions Prof. Mashimo, while talking about his motivation behind the study. The article was published in the Nature Biotechnology journal on January 05, 2026.
The CRISPR–Cas3 system has fundamental structural and functional differences when compared to the CRISPR–Cas9 system. In CRISPR–Cas9, a small fragment of RNA, another genetic material, is used as a guide. This guide RNA (gRNA) binds to the target DNA sequence, and the Cas9 protein bound to the gRNA, acts like a molecular scissor and cuts the DNA. However, a multiprotein cascade complex is involved in the CRISPR–Cas3 system, which acts like a guide for the associated Cas3 helicase–nuclease enzyme, which shreds large DNA regions unidirectionally. This long-range degradation strategy is different from the precise double-strand break technology seen in the CRISPR–Cas9 system.
As TTR is mainly expressed in the liver, the study wanted to understand the efficacy of CRISPR–Cas3 in controlling hepatic TTR expression. A mouse model of ATTR and a lipid nanoparticle (LNP)-based delivery system were used for the study. Results showed that the CRISPR–Cas3 system can induce reliable, extensive deletions of the TTR gene. “Through CRISPR RNA optimization, we achieved around 59% editing at the TTR locus in our in vitro experiments. In mice model, a single LNP-based treatment helped us to achieve more than 48% hepatic editing and reduced serum TTR levels by 80%,” highlights Prof. Mashimo. This system did not induce indels at the off-target sites, which is considered a major limitation for the CRISPR–Cas9 system.
The findings of this study can influence societal perspectives on genetic therapies by highlighting a safer alternative to CRISPR–Cas9, as it avoids the risk of generating unintended, potentially harmful mutant proteins. With further optimization and safety evaluation, this CRISPR–Cas3 can be established as a new and safer platform for genome-editing-based therapies, providing patients with durable, possibly one-time treatments that directly address the root genetic causes of their conditions. This can ultimately improve both life expectancy and quality of life for many individuals.
“In the coming years, this technology can lead to clinical applications not only for ATTR, but also for other currently incurable inherited diseases,” explains Prof. Mashimo as the future of this technology.
Amyloidosis
In a new study, the researchers have shown that the CRISPR–Cas3 system can induce reliable, extensive deletions of the transthyretin (TTR) gene and reduce production of TTR protein without any unintended DNA cuts. The results highlight its potential as an efficient genome-editing system that can be used to cure transthyretin amyloidosis (ATTR), a progressive disorder involving amyloid deposits of misfolded TTR proteins and other genetic disorders.
Reference
Journal：Nature Biotechnology
Title of original paper：
CRISPR–Cas3-based editing for targeted deletions in a mouse model of transthyretin amyloidosis
DOI：
10.1038/s41587-025-02949-6
Authors：
Saeko Ishida1, Yusuke Sato2, Keisuke Chosa1,3, Eri Ezawa1, Yuko Yamauchi1, Masaaki Oyama4, Hiroko Kozuka-Hata4, Rina Ito2, Rikako Sato2, Masatoshi Maeki5, Tomo-o Ishikawa6, Kenichi Yamamura7, Kohei Takeshita8,9, Kensuke Yamaguchi10, Yuta Kochi11, Fumitaka Hashiya12, Yiwei Liu13, Naoko Abe13, Hiroshi Abe13,14, Yoshiki Sekijima15, Kazuto Yoshimi1,16, and Tomoji Mashimo1,16
Affiliations：
1Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Japan
2Laboratory for Molecular Design of Pharmaceutics, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan
3C4U Corporation, Japan
4Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Japan
5Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Japan
6Transgenic, Inc., Japan
7Transgenic Group, Inc., Japan
8Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Japan
9Department of Life Science, University of Hyogo, Japan
10Biomedical Engineering Research Innovation Center, Laboratory for Biomaterials and Bioengineering, Institute of Integrated Research, Institute of Science Tokyo, Japan
11Department of Genomic Function and Diversity, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, Japan
12Research Center for Materials Science, Nagoya University, Japan
13Department of Chemistry, Graduate School of Science, Nagoya University, Japan
14Institute for Glyco-core Research (iGCORE), Nagoya University, Japan
15Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Japan
16Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Japan
2Laboratory for Molecular Design of Pharmaceutics, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan
3C4U Corporation, Japan
4Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Japan
5Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Japan
6Transgenic, Inc., Japan
7Transgenic Group, Inc., Japan
8Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Japan
9Department of Life Science, University of Hyogo, Japan
10Biomedical Engineering Research Innovation Center, Laboratory for Biomaterials and Bioengineering, Institute of Integrated Research, Institute of Science Tokyo, Japan
11Department of Genomic Function and Diversity, Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, Japan
12Research Center for Materials Science, Nagoya University, Japan
13Department of Chemistry, Graduate School of Science, Nagoya University, Japan
14Institute for Glyco-core Research (iGCORE), Nagoya University, Japan
15Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Japan
16Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Japan
About the Institute of Medical Science, The University of Tokyo
The Institute of Medical Science, The University of Tokyo (IMSUT), established in 1892 as the Institute of Infectious Diseases and renamed IMSUT in 1967, is a leading research institution with a rich history spanning over 130 years. It focuses on exploring biological phenomena and disease principles to develop innovative strategies for disease prevention and treatment. IMSUT fosters a collaborative, interdisciplinary research environment and is known for its work in genomic medicine, regenerative medicine, and advanced medical approaches like gene therapy and AI in healthcare. It operates core research departments and numerous specialized centers, including the Human Genome Center and the Advanced Clinical Research Center, and is recognized as Japan’s only International Joint Usage/Research Center in life sciences.About Professor Tomoji Mashimo from the Institute of Medical Science, The University of Tokyo
About Professor Tomoji Mashimo from the Institute of Medical Science, The University of Tokyo Dr. Tomoji Mashimo is a Professor associated with the Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo. Dr. Mashimo received his Ph.D. degree from Kyoto university. His research interest includes genome- editing techniques, particularly CRISPR-Cas-based systems. He has authored more than 150 papers and published more than 20 books till date. Dr. Mashimo is currently the President of the Japanese Genome Editing Society.Funding information
This research was supported in part by the Japan Agency for Medical Research and Development (grant no. JP23bm1223009h0001) to Tomoji Mashimo and Japan Society for the Promotion of Science KAKENHI (grant no. 23H00367) to Tomoji Mashimo.Media contact
Affiliation: Project Coordination Office, The Institute of Medical Science, The University of Tokyohttps://www.ims.u-tokyo.ac.jp/