Article
Medicine, Research & Experimental
Matteo Rossi, Mikhail Steklov, Fanny Huberty, Thuy Nguyen, Jerome Marijsse, Celine Jacques-Hespel, Paul Najm, Caroline Lonez, Eytan Breman
Summary: Genome engineering technologies are powerful tools for optimizing cell functionality. A microRNA-based multiplex shRNA platform can deliver multiple shRNA-like sequences, allowing for precise modulation of target genes.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Biochemistry & Molecular Biology
Chengpeng Wang, Yang Li, Na Wang, Qin Yu, Yonghong Li, Junping Gao, Xiaofeng Zhou, Nan Ma
Summary: We established a platform for CRISPR/Cas9-mediated gene editing in rose using suspension cells, and successfully edited a gene involved in the ethylene signaling pathway. Our optimized CRISPR/Cas9 system provides a powerful tool for functional genomics, molecular breeding, and synthetic biology in rose.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chaya T. L. Yuen, Dawn G. L. Thean, Becky K. C. Chan, Peng Zhou, Cynthia C. S. Kwok, Hoi Yee Chu, Maggie S. H. Cheung, Bei Wang, Yee Man Chan, Silvia Y. L. Mak, Anskar Y. Leung, Gigi C. G. Choi, Zongli Zheng, Alan S. L. Wong
Summary: Researchers have enhanced editing accuracy and reduced off-target edits by re-engineering KKH-SaCas9 with a Y239H mutation and a set of additional mutations, demonstrating the feasibility of multi-domain combinatorial mutagenesis to optimize editing fidelity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Mohamed Ramadan, Muna Alariqi, Yizan Ma, Yanlong Li, Zhenping Liu, Rui Zhang, Shuangxia Jin, Ling Min, Xianlong Zhang
Summary: By optimizing the CRISPR/Cas9 system, 112 plant development-related genes were successfully knocked out in a single experiment. Using a pooled sgRNAs assembly method, over 800 plants were generated, all of which covered the targeted genes. Different sgRNA insertions resulted in various combinations of phenotypes in plant tissues.
Article
Biotechnology & Applied Microbiology
Rajveer Singh, Shivani Chandel, Arijit Ghosh, Anupam Gautam, Daniel H. Huson, V. Ravichandiran, Dipanjan Ghosh
Summary: In the past two decades, yeast has been widely used as a cost-effective biological tool for producing small molecules and biofuels. The application of CRISPR-Cas techniques in yeast genetic and metabolic engineering has revolutionized the field, particularly in targeted chromosomal integration using synthetic donor constructs. This study presents a highly efficient strategy for targeted chromosomal integration and in-frame expression of foreign genes in the yeast genome using CRISPR-Cas9 and homology-dependent recombination (HDR). The optimized methods achieved a 74% efficiency in integrating small constructs at multiple target sites. The study also demonstrated that as few as 15 base pairs of microhomology are sufficient for targeted knock-in with minimal construct concentration. Whole-genome sequencing confirmed the absence of off-target effects. This protocol provides a comprehensive and streamlined approach for integrating essential genes into the yeast genome for synthetic biology and industrial purposes.
Article
Chemistry, Multidisciplinary
Yanjiao Han, Zhefan Yuan, Sijin Luo Zhong, Haoxian Xu, Shaoyi Jiang
Summary: The CRISPR-Cas9 system is a powerful genome-editing tool used in various applications. However, the high-frequency mutations caused by Cas9 at unintended sites pose a major concern for therapeutic applications. Off-target events primarily result from non-specific mismatch between the guide RNA (sgRNA) and target DNA. This study presents two novel methods, involving chemical conjugation of Cas9 with zwitterionic pCB polymers and genetic fusion of Cas9 with zwitterionic (EK)(n) peptides, to minimize this mismatch issue. The modified CRISPR/Cas9 ribonucleoproteins (RNPs) exhibit reduced off-target DNA editing while maintaining on-target gene editing activity. The off-target efficiency of the modified CRISPR/Cas9 is reduced by an average of 70% and up to 90% compared to the unmodified CRISPR/Cas9 editing. These approaches provide a simple and effective way to enhance the development of CRISPR/Cas9-based genome editing for various biological and therapeutic applications.
Article
Virology
Yujia Liu, Dongbin Chen, Xiaoqian Zhang, Shuqing Chen, Dehong Yang, Linmeng Tang, Xu Yang, Yaohui Wang, Xingyu Luo, Manli Wang, Zhihong Hu, Yongping Huang
Summary: This study constructed an inducible CRISPR/Cas9 system specifically targeting Bombyx mori nucleopolyhedrovirus (BmNPV), which enhanced the silkworm's resistance to the virus without affecting its economic traits.
Article
Multidisciplinary Sciences
Zsolt Bodai, Alena L. Bishop, Valentino M. Gantz, Alexis C. Komor
Summary: Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. This study introduces a general strategy called the double tap method, which improves HDR-mediated precision editing efficiency by taking advantage of the reproducible nature of indel sequences. The method utilizes multiple gRNAs, including a primary gRNA that targets the wild-type genomic sequence and one or more secondary gRNAs that target the most common indel sequence(s).
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Ziying Hu, Chengdong Zhang, Shuai Wang, Siqi Gao, Jingjing Wei, Miaomiao Li, Linghui Hou, Huilin Mao, Yanyan Wei, Tao Qi, Hongmao Liu, Dong Liu, Feng Lan, Daru Lu, Hongyan Wang, Jixi Li, Yongming Wang
Summary: This study identified three compact Cas9 orthologs for mammalian genome editing, with SlugCas9 showing comparable activity to SaCas9 and recognizing a simple NNGG PAM. A SlugCas9-SaCas9 chimeric nuclease was generated with high specificity and activity, and a high-fidelity variant of SlugCas9 was engineered while maintaining high specificity without compromising on-target editing efficiency. These minimal Cas9 tools are ideal for both basic research and clinical applications.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Florian Stoertz, Peter Minary
Summary: With the advancement of CRISPR/Cas programmable nuclease system, in vivo therapeutic gene editing applications are becoming more feasible. However, concerns over non-negligible off-target effects remain prominent. crisprSQL is an interactive collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching cleavage profiling, gene editing safety analysis, and transcriptomics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Materials Science, Biomaterials
Jihyun Park, Seong Jae Kang, Seulgi Go, Jeongmin Lee, Jinsu An, Hak Suk Chung, Cherlhyun Jeong, Dae-Ro Ahn
Summary: In order to improve the efficiency and cost-effectiveness of RNA guides, a split-tracrRNA system was developed by nicking the long 67-mer tracrRNA. The shortened tracrRNA(41 + 23), created by nicking in stem loop 2, showed comparable gene editing efficiency and specificity to the full-length tracrRNA(67). Removal of the loop in stem loop 2 was also possible without compromising efficiency and specificity when the stem duplex was stabilized via a high GC content. Binding assays and single-molecule experiments suggested that efficient split-tracrRNAs could be engineered as long as their binding affinity to Cas9 and their reaction kinetics are similar to those of tracrRNA(67).
BIOMATERIALS SCIENCE
(2023)
Article
Multidisciplinary Sciences
E. A. Moreb, M. D. Lynch
Summary: The link between gRNA sequence and Cas9 activity primarily depends on the time it takes for Cas9 to find the target site, which is influenced by species-specific factors. The ability of the Cas9/gRNA complex to locate the target site rather than activity at the target site largely drives sequence-dependent differences in gRNA activity between species.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Katarzyna Balon, Adam Sheriff, Joanna Jackow, Lukasz Laczmanski
Summary: This article describes recent advancements in cancer-selective treatments based on the CRISPR/Cas9 system, including strategies for targeted delivery of the CRISPR/Cas9 machinery to affected cells, controlling Cas9 expression in tissues of interest, and disrupting cancer-specific genes to result in selective death of malignant cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Hao Yu, Liangxue Lai, Zhanjun Li
Summary: Researchers have revisited and engineered a compact Cas9 orthologue derived from Neisseria cinerea (NcCas9) for efficient genome editing in mammal cells. NcCas9 can recognize a PAM sequence (N4GYAT) that existing Cas9s cannot, and by optimizing its architecture and spacer length, editing efficacy is improved. NcCas9-derived Base editors can efficiently generate base conversions, and six anti-CRISPR proteins were identified as off-switches for NcCas9. NcCas9 successfully generated efficient editing of mouse embryos by microinjection of NcCas9 mRNA and the corresponding sgRNA.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Ruosen Xie, Xiuxiu Wang, Yuyuan Wang, Mingzhou Ye, Yi Zhao, Brian S. Yandell, Shaoqin Gong
Summary: This study reports the development of a facilely fabricated pH-responsive polymer nanoparticle for safe and efficient delivery of CRISPR-associated protein 9 (Cas9) for gene editing. These nanoparticles possess many desirable properties, making them potential candidates for clinical applications in genome editing.
ADVANCED MATERIALS
(2022)
Article
Cell Biology
Christopher Minteer, Marco Morselli, Margarita Meer, Jian Cao, Albert Higgins-Chen, Sabine M. Lang, Matteo Pellegrini, Qin Yan, Morgan E. Levine
Summary: This study demonstrates that physiologically relevant aging changes can be induced in vitro and used to uncover mechanistic insights into epigenetic aging.
Article
Cell Biology
Meiling Zhang, Zongzhi Z. Liu, Keisuke Aoshima, Wesley L. Cai, Hongyin Sun, Tianrui Xu, Yangyi Zhang, Yongyan An, Jocelyn F. Chen, Lok Hei Chan, Asako Aoshima, Sabine M. Lang, Zhenwei Tang, Xuanlin Che, Yao Li, Sara J. Rutter, Veerle Bossuyt, Xiang Chen, Jon S. Morrow, Lajos Pusztai, David L. Rimm, Mingzhu Yin, Qin Yan
Summary: Transcriptomic analysis revealed that upregulation of CECR2 is associated with breast cancer metastasis and immune suppression. In mouse models, increased expression of CECR2 promotes breast cancer metastasis. Mechanistically, RELA, a member of the NF-kappa B family, recruits CECR2 to activate the expression of metastasis-related genes.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Farshad Farshidfar, Kahn Rhrissorrakrai, Chaya Levovitz, Cong Peng, James Knight, Antonella Bacchiocchi, Juan Su, Mingzhu Yin, Mario Sznol, Stephan Ariyan, James Clune, Kelly Olino, Laxmi Parida, Joerg Nikolaus, Meiling Zhang, Shuang Zhao, Yan Wang, Gang Huang, Miaojian Wan, Xianan Li, Jian Cao, Qin Yan, Xiang Chen, Aaron M. Newman, Ruth Halaban
Summary: Despite being the most common melanoma subtype among non-White individuals, the molecular drivers of acral melanoma remain unknown. In this study, the authors integrated genomic and clinical data from 104 patients and identified recurrent amplifications of cytoband 22q11.21 and LZTR1 as a key tumor promoter in this region.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Multidisciplinary Sciences
Lok Hei Chan, Qin Yan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Qian Xiao, Xinyan Zhang, Liqun Tu, Jian Cao, Christian S. Hinrichs, Xiaolei Su
Summary: The activation of CAR-T cells is dependent on the size difference between the CAR-antigen pair and CD45. Increasing the size of CAR extracellular domains weakens CAR-T activation, while membrane-proximal epitopes activate CAR-Ts better than membrane-distal epitopes.
SCIENCE IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Hui Zheng, Lizhen Wu, Qian Xiao, Xin Meng, Alex Hafiz, Qin Yan, Renquan Lu, Jian Cao
Summary: DNA sensing through the cGAS-STING pathway is important in cancer immunosurveillance. Activation of STING in the tumor environment is an attractive approach to induce anti-tumor immunity, but it is limited due to epigenetic silencing of STING in many tumors. In this study, the inhibition of KDM5 family histone demethylases restored STING expression in breast cancer cells and activated the cGAS-STING pathway, showing the potential of KDM5 inhibitors as novel immune modulators in cancer therapies.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Review
Oncology
Goran Micevic, Marcus W. Bosenberg, Qin Yan
Summary: Immune checkpoint inhibitors (ICI) have shown significant improvements in treating various cancers, but there are still challenges to overcome. Some cold tumor types, like pancreatic cancer, have low response rates to ICI due to low immunogenicity. Additionally, patients who initially respond to ICI may experience T-cell exhaustion, leading to a lack of sustained response. Recent studies have highlighted the role of epigenetic modifiers in regulating tumor cell immunity and T-cell exhaustion, suggesting that targeting the intersection of epigenetics and immune checkpoint therapy could enhance antitumor immune responses.
CLINICAL CANCER RESEARCH
(2023)
Article
Immunology
Yuanyue Zhang, Jacob T. Bailey, En Xu, Kunal Singh, Marieke Lavaert, Verena M. Link, Shanti D'Souza, Alex Hafiz, Jian Cao, Gaoyuan Cao, Derek B. Sant'Angelo, Wei Sun, Yasmine Belkaid, Avinash Bhandoola, Dorian B. McGavern, Qi Yang
Summary: The study demonstrates that MAIT cells in the meninges play a crucial role in preventing reactive oxidative species accumulation and preserving meningeal barrier integrity.
Article
Genetics & Heredity
Jin Wei, Ajinkya Patil, Clayton K. Collings, Mia Madel Alfajaro, Yu Liang, Wesley L. Cai, Madison S. Strine, Renata B. Filler, Peter C. DeWeirdt, Ruth E. Hanna, Bridget L. Menasche, Arya Okten, Mario A. Pena-Hernandez, Jon Klein, Andrew McNamara, Romel Rosales, Briana L. McGovern, M. Luis Rodriguez, Adolfo Garcia-Sastre, Kris M. White, Yiren Qin, John G. Doench, Qin Yan, Akiko Iwasaki, Thomas P. Zwaka, Jun Qi, Cigall Kadoch, Craig B. Wilen
Summary: This study demonstrates that the activity of the chromatin remodeling complex mSWI/SNF plays an important role in determining susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, highlighting it as a potential therapeutic target for SARS-CoV-2.
Article
Biochemistry & Molecular Biology
Madison S. Strine, Wesley L. Cai, Jin Wei, Mia Madel Alfajaro, Renata B. Filler, Scott B. Biering, Sylvia Sarnik, Ryan D. Chow, Ajinkya Patil, Kasey S. Cervantes, Clayton K. Collings, Peter C. DeWeirdt, Ruth E. Hanna, Kevin Schofield, Christopher Hulme, Silvana Konermann, John G. Doench, Patrick D. Hsu, Cigall Kadoch, Qin Yan, Craig B. Wilen
Summary: Identifying host genes essential for SARS-CoV-2 can reveal potential drug targets and advance our understanding of COVID-19. This study demonstrates that DYRK1A regulates the expression of ACE2 and DPP4, influencing the entry of multiple highly pathogenic human coronaviruses. The findings have significant implications for the development of therapeutic strategies against coronavirus infections.
Article
Oncology
Fernando J. de Miguel, Claudia Gentile, William W. Feng, Shannon J. Silva, Akshay Sankar, Francisco Exposito, Wesley L. Feng, Mary Ann Melnick, Camila Robles-Oteiza, Madeline M. Hinkley, Jeanelle A. Tsai, Antja-Voy Hartley, Jin Wei, Anna Wurtz, Fangyong Li, Maria I. Toki, David L. Rimm, Robert Homer, Craig B. Wilen, Andrew Z. Xiao, Jun Qi, Qin Yan, Don X. Nguyen, Pasi A. Janne, Cigall Kadoch, Katerina A. Politi
Summary: In this study, the chromatin accessibility and gene regulatory signatures of osimertinib-sensitive and resistant EGFR-mutant lung cancer models were investigated. The research discovered the involvement of mammalian SWI/SNF chromatin remodeling complexes in TKI resistance. By disrupting the mSWI/SNF ATPases SMARCA4/SMARCA2, the resistant models were re-sensitized to osimertinib via inhibition of mSWI/SNF-mediated regulation of cellular programs.
Article
Microbiology
Jin Wei, Mia Madel Alfajaro, Wesley L. L. Cai, Vincent R. R. Graziano, Madison S. S. Strine, Renata B. B. Filler, Scott B. B. Biering, Sylvia A. A. Sarnik, Sonam Patel, Bridget L. L. Menasche, Susan R. R. Compton, Silvana Konermann, Patrick D. D. Hsu, Robert C. C. Orchard, Qin Yan, Craig B. B. Wilen
Summary: The histone demethylase KDM6A promotes diverse coronavirus infection by regulating the expression of ACE2, DPP4, and Ceacam1. The KDM6A-KMT2D-p300 complex localizes to enhancer regions of ACE2 and regulates receptor expression. Inhibition of p300 catalytic activity prevents ACE2 and DPP4 expression and confers resistance to SARS-CoV-2 variants and MERS-CoV.
Article
Oncology
Gang Peng, Yibo Xi, Chiara Bellini, Kien Pham, Zhen W. Zhuang, Qin Yan, Man Jia, Guilin Wang, Lingeng Lu, Moon-Shong Tang, Hongyu Zhao, He Wang
Summary: Epigenomic-wide DNA methylation profiling has the potential to reflect risks associated with electronic cigarette exposure and individual poor health outcomes. Our study in male ApoE-/- mice reveals significant alterations in CpG sites after electronic cigarette exposure, with a high percentage annotated with known genes. Pathway analysis indicates activation of MAPK and cardiomyocyte-related signaling pathways, suggesting potential cell-damaging effects of prolonged e-cigarette inhalation.
AMERICAN JOURNAL OF CANCER RESEARCH
(2022)