Article
Medicine, Research & Experimental
Yujie Liang, Xiao Xu, Limei Xu, Zoya Iqbal, Kan Ouyang, Huawei Zhang, Chunyi Wen, Li Duan, Jiang Xia
Summary: This study developed a specific delivery vehicle for gene editing in chondrocytes to attenuate cartilage damage. The results showed that the hybrid delivery vehicle successfully delivered the gene plasmids and suppressed the expression of specific genes in chondrocytes, leading to a decrease in cartilage degradation. This research contributes to alleviating the symptoms and damage of osteoarthritis.
Review
Pharmacology & Pharmacy
Siwei Chen, Deng Chen, Bin Liu, Hidde J. Haisma
Summary: CRISPR/Cas9-mediated genome engineering has extensive applications in basic biology, biotechnology, and medicine. However, the low gene modification efficiency and uncontrollable prolonged Cas9 activity hinder its further use. Researchers have explored small molecules with clinical potential to precisely modulate CRISPR/Cas9 genome editing activity.
DRUG DISCOVERY TODAY
(2022)
Review
Biochemistry & Molecular Biology
Michael J. Thomson, Sudip Biswas, Nikolaos Tsakirpaloglou, Endang M. Septiningsih
Summary: Advances in molecular technologies have provided more powerful plant breeding approaches, and the establishment of efficient CRISPR-Cas-based gene editing promises to bridge the gap between forward genetics and reverse genetics, and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Clarissa Patrizi, Manel Llado, Daniela Benati, Carolina Iodice, Elena Marrocco, Rosellina Guarascio, Enrico M. Surace, Michael E. Cheetham, Alberto Auricchio, Alessandra Recchia
Summary: RP is a progressive retinal degenerative disease causing blindness, and CRISPR/Cas9 can selectively target specific variants for gene editing to restore partial retinal function.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biology
Xiaozhen Liu, Jing Qiao, Ruixuan Jia, Fan Zhang, Xiang Meng, Yang Li, Liping Yang
Summary: This study developed a gene-editing therapeutic drug to selectively target the mutant allele of the RHO gene, which is a common cause of genetic retinitis pigmentosa. In vitro and in vivo experiments demonstrated that this drug was highly specific and effective in improving retinal function and preserving photoreceptors in a mouse model. The study provides strong support for the further development of this therapeutic drug for treating retinitis pigmentosa and offers a framework for developing gene-editing medicines.
Article
Multidisciplinary Sciences
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna
Summary: The fusion of PRDM9 and Cas9 in CRISPR-Cas genome editing can increase the efficiency of homology-directed repair (HDR) and avoid off-target editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemical Research Methods
Aidan R. O'Brien, Gaetan Burgio, Denis C. Bauer
Summary: This review discusses the challenges and common considerations of using machine learning in CRISPR gene editing applications, providing concrete examples from the genome engineering domain. The authors emphasize the importance of equipping researchers with the knowledge to effectively use machine learning to improve experimental design and predict outcomes, ultimately accelerating the advancement of the field.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Xueli Zhang, Chaohui Zhang, Caijiao Liang, Bizhou Li, Fanmei Meng, Yuncan Ai
Summary: Bacteriophages, the most abundant organisms in the biosphere, have been sequenced extensively. However, the study of bacteriophage functional genomics has been hindered by a lack of effective research methods. This study designed a phage genome editing platform based on the CRISPR-Cas9 system, and successfully achieved gene editing in Vibrio natriegens phage TT4P2. This platform has the potential to advance research on phage gene diversity and accelerate the development of phage synthetic biology and nanotechnology.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Koray Malci, Nestor Jonguitud-Borrego, Hugo van der Straten Waillet, Urte Puodziunaite, Emily J. Johnston, Susan J. Rosser, Leonardo Rios-Solis
Summary: This study presents a simplified method for yeast genome editing, called ACtivE, which relies on in vivo assembly of linear DNA fragments. By eliminating preassembled DNAs and extra cloning steps, this method improves the efficiency and convenience of genome editing. Through optimization, high integration efficiency was achieved, providing well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Article
Multidisciplinary Sciences
Joonbum Lee, Dong-Hwan Kim, Madeline C. Karolak, Sangsu Shin, Kichoon Lee
Summary: In this study, we successfully generated genome-edited chicken and duck lines without the conventional PGC-mediated procedures by injecting an adenovirus containing the CRISPR-Cas9 system into avian blastoderms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Agriculture, Dairy & Animal Science
Julia Popova, Victoria Bets, Elena Kozhevnikova
Summary: Genome editing has practical applications in farm animals, improving production traits, economic value, and disease resistance. It also has potential in biomedical research and drug production, as well as xenograft donors. Recent advancements in site-specific nucleases and embryological delivery methods have revolutionized transgenesis, providing efficient and reliable tools for genome engineering in agriculture.
Article
Oncology
Alexandra G. Kouroukli, Nivethika Rajaram, Pavel Bashtrykov, Helene Kretzmer, Reiner Siebert, Albert Jeltsch, Susanne Bens
Summary: The study demonstrates the feasibility of silencing TERT alleles using allele-specific epigenome editing. This new strategy may have important advantages in cancer treatment, such as reducing adverse side effects.
CLINICAL EPIGENETICS
(2023)
Article
Multidisciplinary Sciences
Yao Wang, Tao Qi, Jingtong Liu, Yuan Yang, Ziwen Wang, Ying Wang, Tianyi Wang, Miaomiao Li, Mingqing Li, Daru Lu, Alex Chia Yu Chang, Li Yang, Song Gao, Yongming Wang, Feng Lan
Summary: The CRISPR-Cas system can treat autosomal dominant diseases by disrupting mutant alleles through nonhomologous end joining (NHEJ). However, current CRISPR-Cas systems cannot differentiate many single-nucleotide mutations from wild-type alleles. We identified Cas12j-8 as an ideal genome editor with comparable activity to AsCas12a and Un1Cas12f1. Cas12j-8 is a highly specific nuclease sensitive to single-nucleotide mismatches in the protospacer adjacent motif (PAM)-proximal region. It enables allele-specific disruption of genes with single-nucleotide polymorphisms (SNPs) and has potential therapeutic applications.
Article
Biochemistry & Molecular Biology
Ahmed K. Mahdi, Juan F. Medrano, Pablo J. Ross
Summary: We investigated the possibility of single-step genome editing in small ruminants using CRISPR-Cas9 zygote electroporation. We found that electroporation was more efficient than microinjection and successfully disrupted target genes in sheep and goat embryos.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Takashi Takeda, Yuhki Yokoyama, Hidekazu Takahashi, Daisuke Okuzaki, Kaho Asai, Hiroaki Itakura, Norikatsu Miyoshi, Shogo Kobayashi, Mamoru Uemura, Toshitsugu Fujita, Hiroo Ueno, Masaki Mori, Yuichiro Doki, Hodaka Fujii, Hidetoshi Eguchi, Hirofumi Yamamoto
Summary: The study aimed to unravel the regulatory mechanism of the KLF5 gene product in CRC through in vitro methods, revealing that KLF5 protein constructs a core-regulatory circuitry with co-factors in the three-dimensional genome structure and coordinately regulates KLF5 and CCAT1 expression in CRC.
BRITISH JOURNAL OF CANCER
(2022)
Article
Genetics & Heredity
Ashita Sarudate, Toshitsugu Fujita, Takahiro Nakayama, Hodaka Fujii
Summary: This study developed a method called enChIP-Seq to detect physical interactions between genomic regions. It combines engineered DNA-binding molecule-mediated chromatin immunoprecipitation and next-generation sequencing analysis. The researchers also developed enChIP-Seq analyzer software to facilitate the analysis of enChIP-Seq data and identify specific interactions between genomic regions.
Article
Cell Biology
Hirotaka Fujita, Toshitsugu Fujita, Hodaka Fujii
Summary: This study assessed the role of inhibitor of nuclear factor-kappa B kinases (IKKs) in the regulation of interleukin-3 (IL-3)-mediated immediate early gene expression. The results showed that IKK1 and IKK2 are necessary for the immediate expression of c-fos and c-jun induced by IL-3. In addition, IKK2 plays an important role in the activation of c-Jun N-terminal kinase (JNK). The findings suggest that the IKK2-JNK axis regulates IL-3-induced immediate early gene expression in a canonical NF-kappa B-independent manner.
Article
Pathology
Sachiko Imanishi, Shoko Nagata, Toshitsugu Fujita, Hodaka Fujii
Summary: Hepatocellular carcinoma (HCC) is a common and deadly form of liver cancer. Current biomarkers for HCC diagnosis lack specificity, necessitating the search for more specific biomarkers. Recent research has identified circRNA as a potential biomarker for specific HCC diagnosis. Using publicly available RNA-seq data, this study identified eight circRNAs with altered expression levels in HCC tissues. Two circRNAs (hsa_circ_0001438 and hsa_circ_0000417) were identified as potential biomarkers for specific HCC diagnosis.
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY
(2022)
Article
Chemistry, Analytical
Toshitsugu Fujita, Shoko Nagata, Hodaka Fujii
Summary: Blocking PCR is a method to selectively inhibit the amplification of wild-type DNA while amplifying mutated DNA by using a nucleotide sequence complementary to a blocker. Our study demonstrates that an oligoribonucleotide (ORN) can effectively suppress the extension of target DNA by Taq DNA polymerases. This method has been successfully applied for real-time ORNi-PCR and one-step real-time reverse transcriptionORNi-PCR to detect single-nucleotide mutations in DNA and RNA in a sequence-specific manner, providing technical insights for further improvement of blocking PCR.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Minako Yokoyama, Toshitsugu Fujita, Yuka Kadonosawa, Yota Tatara, Daisuke Motooka, Masahito Ikawa, Hodaka Fujii, Yoshihito Yokoayama
Summary: CBR1 is a nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase with broad substrate specificity. This study generated transgenic mice overexpressing CBR1 and characterized the expression of CBR1 in various organs, as well as identified changes in protein expression patterns. The transgenic mice may be useful for further understanding the molecular mechanisms regulated by CBR1 and its effects on carcinogenesis and cardiotoxicity of certain cancer drugs.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Gastroenterology & Hepatology
Xiaolong Zhang, Pankaj Sharma, Patrick Maschmeyer, Yu Hu, Mumeng Lou, Jessica Kim, Hodaka Fujii, Derya Unutmaz, Robert F. Schwabe, Florian Winau
Summary: The expression of GARP on hepatic stellate cells (HSCs) drives the development of liver fibrosis through cell contraction-mediated activation of latent TGF-I3. This finding highlights the potential of GARP on HSCs as a promising target for the treatment of liver fibrosis.
JOURNAL OF HEPATOLOGY
(2023)
Article
Biochemical Research Methods
Toshitsugu Fujita, Shoko Nagata, Miyuki Yuno, Hodaka Fujii
Summary: The CRISPR/dCas13a RNP complex can specifically inhibit reverse transcription (RT) reactions by using a chemically synthesized gRNA sequence, which may be useful for assessing target binding activity, discriminating RNA species retaining gRNA, or suppressing RT from undesirable RNA species.
BIOLOGY METHODS & PROTOCOLS
(2021)
Article
Biochemical Research Methods
Hodaka Fujii, Toshitsugu Fujita
Summary: The article describes a method to purify specific genomic regions and identify associated molecules using enChIP technology. By tagging the target genomic region with variants of the CRISPR system, successful expression was achieved in budding yeast. This method has the potential for analyzing genome functions and conducting CRISPR experiments.
BIOLOGY METHODS & PROTOCOLS
(2022)
Review
Biochemical Research Methods
Takeshi Shimizu, Toshitsugu Fujita, Hodaka Fujii
Summary: ORNi-PCR technology utilizes short RNA to interfere with PCR amplification of specific target sequences, effectively suppressing background signal amplification, and can be used for detecting nucleotide mutations and enriching DNA sequences.
BIOLOGY METHODS & PROTOCOLS
(2022)