Article
Biotechnology & Applied Microbiology
Emanuel Goncalves, Mark Thomas, Fiona M. Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Alessandro Vinceti, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J. Garnett
Summary: MinLibCas9 is an optimized human genome-wide CRISPR-Cas9 library that reduces the size by over 42% compared to other libraries, while maintaining high sensitivity and specificity. This design increases the dynamic range of CRISPR-Cas9 screens, allowing for its application in complex models and assays. MinLibCas9 is also backward compatible with existing datasets.
Article
Biochemistry & Molecular Biology
Shanzhou Huang, Zuyi Ma, Qi Zhou, Aimei Wang, Yuanfeng Gong, Zhenchong Li, Shujie Wang, Qian Yan, Dongping Wang, Baohua Hou, Chuanzhao Zhang
Summary: DUSP4 deficiency mediates Lenvatinib resistance by activating MAPK/ERK signaling, and combination therapy using Lenvatinib and MEK inhibitors may be a promising therapeutic strategy for overcoming Lenvatinib resistance.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Gabriel T. Koreman, Yineng Xu, Qinan Hu, Zijing Zhang, Sarah E. Allen, Mariana F. Wolfner, Bei Wang, Chun Han
Summary: The study addresses the deficiencies of tissue-specific CRISPR/Cas9 tools in Drosophila and proposes corresponding improvements. By optimizing gRNA design, developing methods to label mutant cells, and generating new genetic reagents, the versatility, reliability, and effectiveness of tissue-specific mutagenesis have been enhanced.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
X. -y. Ni, W. -j. Lu, X. Qiao, J. Huang
Summary: The study found that all four promoters could be used with variable efficiency to drive mutagenesis of the white gene in Drosophila suzukii. Among the four DsU6 promoters tested, DsU6-3 had the highest genome editing efficiency. In comparison, the DmU6:3 promoter showed lower efficiency. These findings expand the options for promoters to express gRNAs in D. suzukii, facilitating both basic and applied research on this important pest.
INSECT MOLECULAR BIOLOGY
(2021)
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
Oncology
Jingjing Zhang, Yun Li, Hua Liu, Jiahui Zhang, Jie Wang, Jia Xia, Yu Zhang, Xiang Yu, Jinyan Ma, Masha Huang, Jiahui Wang, Liangzhe Wang, Qian Li, Rutao Cui, Wen Yang, Yingjie Xu, Weiwei Feng
Summary: This study identified PCMT1 as a critical driver of resistance to detachment-induced apoptosis in ovarian cancer cells. PCMT1 enhanced cell migration, adhesion and spheroid formation through interaction with the ECM protein LAMB3. Treatment with an antibody against extracellular PCMT1 reduced cancer cell invasion and adhesion. PCMT1 was highly expressed in late-stage metastatic tumors, suggesting its potential as a therapeutic target in metastatic ovarian cancer.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yicun Wang, Jinhui Wu, Hui Chen, Yang Yang, Chengwu Xiao, Xiaoming Yi, Changjie Shi, Ke Zhong, Haowei He, Yaoming Li, Zhenjie Wu, Guangxin Zhou, Qiu Rao, Xiaoxia Wang, Xiaodie Zhou, Gwen Lomberk, Bing Liu, Jianning Zhao, Jingping Ge, Wenquan Zhou, Xiaoyuan Chu, Cheng Chen, Xuhui Zhou, Linhui Wang, Kunliang Guan, Le Qu
Summary: The study identified KLF11 as a negative regulator in sarcoma cancer stem cells, forming a negative feedback loop with YAP/TEAD. Epigenetic silencing of KLF11 in CSCs leads to sustained YAP activation, which is associated with poor prognosis and chemotherapy response in sarcoma patients. Pharmacological activation of KLF11 effectively restored chemotherapy response.
Article
Biochemistry & Molecular Biology
Shuai Wang, Chen Tao, Huilin Mao, Linghui Hou, Yao Wang, Tao Qi, Yuan Yang, Sang-Ging Ong, Shijun Hu, Renjie Chai, Yongming Wang
Summary: Due to different nucleotide preferences at target sites, no single Cas9 is capable of editing all sequences. Thus, there is a need to establish a Cas9 repertoire covering all sequences for efficient genome editing. In this study, we identified new SaCas9 orthologs with a simple NNGG PAM requirement by comparing the PAM-interacting domains in 16 SaCas9 orthologs. We also discovered three amino acids that determine the NNGG PAM requirement of SaCas9. Furthermore, we engineered high-fidelity versions of Cas9s, Sha2Cas9 and SpeCas9, which displayed high activities and distinct nucleotide preferences. Our findings offer a new perspective for expanding the Cas9 repertoire and identifying SaCas9 orthologs with NNGG PAM requirements.
Article
Materials Science, Multidisciplinary
Yue Wang, Xiujue Zheng, Jun Liu, Qixian Chen, Yan Zhao
Summary: The emergence of CRISPR-based genome editing systems has revolutionized the field of molecular biology and holds great promise for the treatment of various diseases. However, the lack of suitable delivery vehicles for effective intracellular delivery of CRISPR components limits its practical applications. In this study, a nanometer-scaled vesicle platform (CRISPRsome) was developed to efficiently deliver the essential components of the CRISPR system, resulting in significant gene knockout efficacy in cancer cells. This study highlights the potential of CRISPRsome in facilitating the use of CRISPR technology in practical applications.
ACS MATERIALS LETTERS
(2022)
News Item
Multidisciplinary Sciences
Smriti Mallapaty
Summary: Concerns about excessive interference are overshadowing the proposal for protecting children whose genomes were edited.
News Item
Multidisciplinary Sciences
Smriti Mallapaty
Summary: The newly published guidelines will encourage research on crops with improved resistance to climate change.
News Item
Multidisciplinary Sciences
Smriti Mallapaty
Summary: He Jiankui's refusal to discuss his controversial 2018 experiments is causing frustration among researchers.
Review
Biochemistry & Molecular Biology
Yulin Mu, Chengxiao Zhang, Taihua Li, Feng-Jie Jin, Yun-Ju Sung, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
Summary: Lactobacillus, important in food production and probiotics, can benefit from CRISPR/Cas9-based genome editing to improve strain efficiency and achieve traceless genome modification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Letter
Oncology
M. Spalato-Ceruso, A. Laroche-Clary, R. Perret, Y. Valverde, V Chaire, Marie-Alix Derieppe, V. Velasco, A. Bourdon, A. Italiano
Summary: Soft-tissue sarcoma (STS) is a rare and heterogeneous group of tumors with limited treatment options and high fatality rates. However, targeting ATM signaling network genes has been found to overcome resistance to ATR inhibition, as demonstrated by our CRISPR/Cas9 knockout models. Furthermore, the combination of ATM inhibitor AZD0156 and ATR inhibitor AZD6738 has shown synergistic effects, significantly inhibiting STS growth in vitro and inducing higher levels of DNA damage.
EXPERIMENTAL HEMATOLOGY & ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Kendall J. Condon, Jose M. Orozco, Charles H. Adelmann, Jessica B. Spinelli, Pim W. van der Helm, Justin M. Roberts, Tenzin Kunchok, David M. Sabatini
Summary: Our study identified a catalog of genes that impact the mTORC1 pathway and clarified the multifaceted ways in which mTORC1 senses mitochondria dysfunction.AMPK and HRI are two of the key kinases that signal mitochondria distress to mTORC1, and their loss renders mTORC1 signaling largely resistant to mitochondria dysfunction induced by various inhibitors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Sabrina M. Heman-Ackah, Raquel Manzano, Jeroen J. M. Hoozemans, Wiep Scheper, Rowan Flynn, Wilfried Haerty, Sally A. Cowley, Andrew R. Bassett, Matthew J. A. Wood
HUMAN MOLECULAR GENETICS
(2017)
Review
Biochemistry & Molecular Biology
Andrew R. Bassett
Article
Biochemistry & Molecular Biology
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinead Collins
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Multidisciplinary Sciences
Qianxin Wu, Quentin R. V. Ferry, Toni A. Baeumler, Yale S. Michaels, Dimitrios M. Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R. Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A. Hollander, Thomas A. Milne, Jin-Soo Kim, Anton J. Enright, Andrew R. Bassett, Tudor A. Fulga
NATURE COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Mattea J. Finelli, Davide Aprile, Enrico Castroflorio, Alexander Jeans, Matteo Moschetta, Lauren Chessum, Matteo T. Degiacomi, Julia Grasegger, Alexis Lupien-Meilleur, Andrew Bassett, Elsa Rossignol, Philippe M. Campeau, Michael R. Bowl, Fabio Benfenati, Anna Fassio, Peter L. Oliver
HUMAN MOLECULAR GENETICS
(2019)
Article
Genetics & Heredity
Elizabeth A. Coe, Jennifer Y. Tan, Michael Shapiro, Pakavarin Louphrasitthiphol, Andrew R. Bassett, Ana C. Marques, Colin R. Goding, Keith W. Vance
Article
Cell Biology
Hugo J. R. Fernandes, Nikolaos Patikas, Stefanie Foskolou, Sarah F. Field, Jong-Eun Park, Meg L. Byrne, Andrew R. Bassett, Emmanouil Metzakopian
Article
Biochemistry & Molecular Biology
Ana Artero-Castro, Kathleen Long, Andrew Bassett, Almudena Avila-Fernandez, Marta Corton, Antonio Vidal-Puig, Pavla Jendelova, Francisco Javier Rodriguez-Jimenez, Eleonora Clemente, Carmen Ayuso, Slaven Erceg
Summary: Hereditary retinal dystrophies are a significant cause of blindness due to lack of effective treatments. Patient-derived human-induced pluripotent stem cells can potentially provide autologous cells for therapy, but the presence of gene mutations remains a challenge.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Jeremy Schwartzentruber, Sarah Cooper, Jimmy Z. Liu, Inigo Barrio-Hernandez, Erica Bello, Natsuhiko Kumasaka, Adam M. H. Young, Robin J. M. Franklin, Toby Johnson, Karol Estrada, Daniel J. Gaffney, Pedro Beltrao, Andrew Bassett
Summary: A genome-wide AD meta-analysis identified 37 risk loci, including new associations near CCDC6, TSPAN14, NCK2, and SPRED2. By fine-mapping SNPs and using functional annotation, 21 SNPs with >50% probability of being causally involved in AD risk were identified. Protein interaction networks and tissue-specific expression helped prioritize genes, leading to the discovery of likely causal genes.
Article
Multidisciplinary Sciences
Qianxin Wu, Chenqu Suo, Tom Brown, Tengyao Wang, Sarah A. Teichmann, Andrew R. Bassett
Summary: INSIGHT is a two-stage COVID-19 testing strategy that combines point-of-care diagnosis with next-generation sequencing to achieve population-scale testing; the first stage provides quick decentralized readout, aiming for early isolation of asymptomatic patients and gives results within 1 to 2 hours; the second stage confirms near-patient testing results and facilitates centralized data collection.
Article
Multidisciplinary Sciences
Isabel E. Wassing, Emily Graham, Xanita Saayman, Lucia Rampazzo, Christine Ralf, Andrew Bassett, Fumiko Esashi
Summary: The study reveals a previously unknown function of RAD51 in promoting genomic stability during mitosis by protecting under-replicated DNA, promoting mitotic DNA synthesis (MiDAS), and successful chromosome segregation.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Adela Pribylova, Lukas Fischer, Douglas E. Pyott, Andrew Bassett, Attila Molnar
Summary: This study investigates the impact of epigenetic modifications, specifically cytosine methylation, on the efficacy of CRISPR/Cas9-induced mutations in plants. It is found that high levels of promoter methylation can decrease the frequency of Cas9-mediated mutations and influence the ratio of insertions and deletions. The study also uncovers a novel type of DNA break and repair mechanism in plant cells.
Article
Biochemistry & Molecular Biology
Sarah Cooper, Jeremy Schwartzentruber, Eve L. Coomber, Qianxin Wu, Andrew Bassett
Summary: Understanding the impact of genetic variation in gene regulatory elements is crucial for interpreting genome function. In this study, a new medium-throughput screening system called GenIE-ATAC was developed to measure the effect of individual variants on chromatin accessibility in their natural genomic and chromatin context. The method was validated in human induced pluripotent stem cells and demonstrated its ability to identify and prioritize causal variants for functional follow-up and understanding regulatory element function mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sarah E. Cooper, Jeremy Schwartzentruber, Erica Bello, Eve L. Coomber, Andrew R. Bassett
NUCLEIC ACIDS RESEARCH
(2020)
Article
Developmental Biology
Alaa Hachem, Jonathan Godwin, Margarida Ruas, Hoi Chang Lee, Minerva Ferrer Buitrago, Goli Ardestani, Andrew Bassett, Sebastian Fox, Felipe Navarrete, Petra de Sutter, Bjorn Heindryckx, Rafael Fissore, John Parrington