Review
Biotechnology & Applied Microbiology
Pratima R. Chennuri, Zach N. Adelman, Kevin M. Myles
Summary: This review summarizes the current state of the art in the development of technologies to prevent the uncontrolled spread of CRISPR-based autonomous homing gene drives.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Sebald A. N. Verkuijl, Joshua X. D. Ang, Luke Alphey, Michael B. Bonsall, Michelle A. E. Anderson
Summary: This article discusses the use of genetic changes to address ecological and public health challenges caused by insect pests. It highlights the development of technologies such as synthetic gene drives and the recent advancements in programmable nucleases like CRISPR-Cas9. The focus is on homing endonuclease gene drives and the challenges involved, as well as strategies to improve their efficiency and mitigate unintended outcomes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Binyou Liao, Xi Chen, Xuedong Zhou, Yujie Zhou, Yangyang Shi, Xingchen Ye, Min Liao, Ziyi Zhou, Lei Cheng, Biao Ren
Summary: Genome editing technology has made rapid progress in recent years. The limitations of traditional gene-editing methods have led to the development of the CRISPR/Cas system, which has become the dominant genomic editing technology in academia and the pharmaceutical industry due to its high efficiency, simple design, and wide applications.
ARCHIVES OF MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Si-Wei Wang, Chao Gao, Yi-Min Zheng, Li Yi, Jia-Cheng Lu, Xiao-Yong Huang, Jia-Bin Cai, Peng-Fei Zhang, Yue-Hong Cui, Ai-Wu Ke
Summary: The CRISPR/Cas9 gene editing technology has made significant progress in oncological research, providing a powerful tool for exploring the mechanism of cancer, establishing tumor models, and studying drug targets.
Article
Gastroenterology & Hepatology
Anna-Lena Scherr, Luisa Nader, Kaiyu Xu, Christin Elssner, Dirk A. Ridder, Federico Nichetti, Manuel Mastel, Sarah Fritzsche, Eblina Kelmendi, Nathalie Schmitt, Paula Hoffmeister-Wittmann, Sofia M. E. Weiler, Felix Korell, Thomas Albrecht, Maximilian Schwab, Hanna Isele, Annika Kessler, Jennifer Huellein, Agnieszka Seretny, Liangtao Ye, Toni Urbanik, Stefan Welte, Anne-Laure Leblond, Christoph E. Heilig, Mohammad Rahbari, Adnan Ali, Suchira Gallage, Benedicte Lenoir, Nina Wilhelm, Ulrike Gaertner, Simon J. Ogrodnik, Christoph Springfeld, Darjus Tschaharganeh, Stefan Froehling, Thomas Longerich, Henning Schulze-Bergkamen, Dirk Jaeger, Lydia Brandl, Peter Schirmacher, Beate K. Straub, Achim Weber, Enrico N. De Toni, Benjamin Goeppert, Mathias Heikenwalder, Rene Jackstadt, Stephanie Roessler, Kai Breuhahn, Bruno C. Koehler
Summary: This study identifies an activation signaling pathway in hepatocellular carcinoma that is prognostically relevant and etiology-independent, which may have important implications for the development and treatment of HCC.
Article
Multidisciplinary Sciences
J. Boutin, J. Rosier, D. Cappellen, F. Prat, J. Toutain, P. Pennamen, J. Bouron, C. Rooryck, J. P. Merlio, I. Lamrissi-Garcia, G. Cullot, S. Amintas, V. Guyonnet-Duperat, C. Ged, J. M. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel
Summary: The study reveals the genotoxicity caused by CRISPR-Cas9 leading to loss of heterozygosity changes, while also highlighting the potential safety concerns of this technology for gene therapy.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Wei Sheng Siew, Yin Quan Tang, Chee Kei Kong, Bey-Hing Goh, Serena Zacchigna, Kamal Dua, Dinesh Kumar Chellappan, Acharaporn Duangjai, Surasak Saokaew, Pochamana Phisalprapa, Wei Hsum Yap
Summary: The CRISPR/Cas system is widely used for studying atherosclerosis and has made significant advances. Different Cas9 variants and other Cas proteins are employed for various applications, including gene editing, gene regulation, and nucleic acid detection. These studies have provided valuable evidence for correcting genes associated with atherosclerosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Pharmacology & Pharmacy
Daniel Allen, Nechama Kalter, Michael Rosenberg, Ayal Hendel
Summary: Genome engineering through targeted nucleases, especially CRISPR-Cas9, has revolutionized gene therapy research and has the potential to treat blood and immune system diseases. CRISPR-Cas9 homology-directed repair (HDR) represents a promising method for site-specific gene insertion or correction. Other methods, like viral gene addition, gene knockout through non-homologous end joining (NHEJ), and base or prime editing, also show promise but have significant limitations for treating genetic immune or blood disorders. This review aims to highlight the transformative benefits of HDR-mediated gene therapy and propose solutions for current challenges, in order to advance HDR-based gene therapy in CD34(+) hematopoietic stem progenitor cells (HSPCs).
Article
Biochemical Research Methods
Vijaydev Ganesan, Lummy Monteiro, Dheeraj Pedada, Anthony Stohr, Mark Blenner
Summary: Yarrowia lipolytica is an industrial host with a high fatty acid flux. In this study, we developed a rapid multiplexed strain engineering tool using base editors for efficient gene editing. The base editors were found to be less toxic than CRISPR-Cas9 for multiplexed gene editing. By optimizing the editing conditions and using a co-selection approach, we achieved high-efficiency multiplexed gene editing.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Cell & Tissue Engineering
Huan Zou, Mingfeng Guan, Yundong Li, Fang Luo, Wenyuan Wang, Yiren Qin
Summary: This study successfully corrected the genetic mutation of Achondroplasia patients using stem cells and gene editing technology, restoring their chondrogenic differentiation ability and providing an important theoretical and experimental basis for Achondroplasia research and treatment.
STEM CELL RESEARCH & THERAPY
(2021)
Article
Clinical Neurology
Serena Mero, Leonardo Salviati, Vincenzo Leuzzi, Anna Rubegni, Cristina Calderan, Francesca Nardecchia, Daniele Galatolo, Maria Andrea Desbats, Valentina Naef, Federica Gemignani, Maria Novelli, Alessandra Tessa, Roberta Battini, Filippo M. Santorelli, Maria Marchese
Summary: Mutations in the COQ4 gene can lead to mitochondrial diseases with diverse clinical presentations. We reported two patients with bi-allelic variants in COQ4, expanding the phenotypic and genetic spectrum, both presenting with motor impairment and ataxia. Functional studies in patient-derived cells and model organisms confirmed the disease relevance of these mutations, providing insights into the role of COQ4 in brain development in vivo.
JOURNAL OF NEUROLOGY
(2021)
Article
Multidisciplinary Sciences
Behnaz Rahmani, Mohammad Hassan Kheirandish, Samaneh Ghanbari, Abbasali Raz, Fahimeh Shamsi, Fatemeh Davami
Summary: This study investigated the use of two small molecules, B02 and Nocodazole, to improve CRIS-PITCh knock-in efficiency. The results showed that Nocodazole had a more significant effect than B02. The findings of this study could be useful for future research in establishing rCHO cell lines.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Yan Zhang, Yupeng Cai, Shi Sun, Tianfu Han, Li Chen, Wensheng Hou
Summary: CRISPR/SaCas9 is an efficient genome editing tool that shows comparable suitability to SpCas9 in soybean, allowing for a wider range of target sequences for genome editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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)
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Dong Niu, Xiang Ma, Taoyan Yuan, Yifan Niu, Yibin Xu, Zhongxin Sun, Yuan Ping, Weifen Li, Jufang Zhang, Tao Wang, George M. Church
Summary: Xenotransplantation of pig organs offers a potential solution to the shortage of donor organs for human patients but faces challenges such as immune rejection and the risk of porcine endogenous retrovirus transmission. Advances in genome engineering and immunosuppressive medications have the potential to overcome these barriers, leading to promising preclinical results and upcoming clinical trials for organs like islet, kidney, and heart transplantation.
ADVANCED DRUG DELIVERY REVIEWS
(2021)
Article
Biochemical Research Methods
Huy Q. Nguyen, Shyamtanu Chattoraj, David Castillo, Son C. Nguyen, Guy Nir, Antonios Lioutas, Elliot A. Hershberg, Nuno M. C. Martins, Paul L. Reginato, Mohammed Hannan, Brian J. Beliveau, George M. Church, Evan R. Daugharthy, Marc A. Marti-Renom, C-ting Wu
Article
Biochemistry & Molecular Biology
Jorge A. Marchand, Merrick D. Pierson Smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church
Summary: T-box riboswitches are a large family of tRNA-binding leader sequences that are crucial for gene regulation in many gram-positive bacteria. TBDB is an open-access database that contains a vast collection of T-box riboswitch sequences and provides structural annotations for this important family of regulatory RNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Engineering, Biomedical
Yanan Yue, Weihong Xu, Yinan Kan, Hong-Ye Zhao, Yixuan Zhou, Xiaobin Song, Jiajia Wu, Juan Xiong, Dharmendra Goswami, Meng Yang, Lydia Lamriben, Mengyuan Xu, Qi Zhang, Yu Luo, Jianxiong Guo, Shengyi Mao, Deling Jiao, Tien Dat Nguyen, Zhuo Li, Jacob V. Layer, Mailin Li, Violette Paragas, Michele E. Youd, Zhongquan Sun, Yuan Ding, Weilin Wang, Hongwei Dou, Lingling Song, Xueqiong Wang, Lei Le, Xin Fang, Haydy George, Ranjith Anand, Shi Yun Wang, William F. Westlin, Marc Guell, James Markmann, Wenning Qin, Yangbin Gao, Hong-Jiang Wei, George M. Church, Luhan Yang
Summary: Genetic engineering of pigs using a combination of CRISPR-Cas9 and transposon technologies allows for inactivation of endogenous retroviruses and enhancement of compatibility with the human immune system, providing a potential pathway for safe and effective porcine xenotransplantation.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Mirko Palla, Sukanya Punthambaker, Benjamin Stranges, Frederic Vigneault, Jeff Nivala, Daniel Wiegand, Aruna Ayer, Timothy Craig, Dmitriy Gremyachinskiy, Helen Franklin, Shaw Sun, James Pollard, Andrew Trans, Cleoma Arnold, Charles Schwab, Colin Mcgaw, Preethi Sarvabhowman, Dhruti Dalal, Eileen Thai, Evan Amato, Ilya Lederman, Meng Taing, Sara Kelley, Adam Qwan, Carl W. Fuller, Stefan Roever, George M. Church
Summary: The use of single-molecule DNA sequencing platform allows for rapid screening of polymerase variants, enabling the identification of enzymes with different features. This approach is valuable for applications requiring polymerases with altered physical properties.
Article
Biotechnology & Applied Microbiology
Alex H. M. Ng, Parastoo Khoshakhlagh, Jesus Eduardo Rojo Arias, Giovanni Pasquini, Kai Wang, Anka Swiersy, Seth L. Shipman, Evan Appleton, Kiavash Kiaee, Richie E. Kohman, Andyna Vernet, Matthew Dysart, Kathleen Leeper, Wren Saylor, Jeremy Y. Huang, Amanda Graveline, Jussi Taipale, David E. Hill, Marc Vidal, Juan M. Melero-Martin, Volker Busskamp, George M. Church
Summary: Using a library of human transcription factor genes, this study identified and utilized new transcription factors to directly program human pluripotent stem cells into various cell types, offering a novel approach in the field of cell engineering.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shilpa Garg, Arkarachai Fungtammasan, Andrew Carroll, Mike Chou, Anthony Schmitt, Xiang Zhou, Stephen Mac, Paul Peluso, Emily Hatas, Jay Ghurye, Jared Maguire, Medhat Mahmoud, Haoyu Cheng, David Heller, Justin M. Zook, Tobias Moemke, Tobias Marschall, Fritz J. Sedlazeck, John Aach, Chen-Shan Chin, George M. Church, Heng Li
Summary: The DipAsm method utilizes long, accurate reads and long-range conformation data to generate chromosome-scale phased assembly for single individuals within a day, demonstrating superior performance in both contiguity and phasing completeness compared to other approaches. DipAsm is crucial for the discovery of structural variants and highly polymorphic and medically important regions, facilitating high-quality precision medicine and studies of individual haplotype variation and population diversity.
NATURE BIOTECHNOLOGY
(2021)
Letter
Multidisciplinary Sciences
Lindsey R. Robinson-McCarthy, Alexander J. Mijalis, Gabriel T. Filsinger, Helena de Puig, Nina M. Donghia, Thomas E. Schaus, Robert A. Rasmussen, Raphael Ferreira, Jeantine E. Lunshof, George Chao, Dmitry Ter-Ovanesyan, Oliver Dodd, Erkin Kuru, Adama M. Sesay, Joshua Rainbow, Andrew C. Pawlowski, Timothy M. Wannier, Peng Yin, James J. Collins, Donald E. Ingber, George M. Church, Jenny M. Tam
Article
Multidisciplinary Sciences
William J. Bradshaw, Ethan C. Alley, Jonathan H. Huggins, Alun L. Lloyd, Kevin M. Esvelt
Summary: Bidirectional tracing is more effective in improving outbreak control and reducing effective reproduction number, compared to forward-tracing alone. Expanding the manual tracing window or implementing smartphone-based exposure notification can significantly increase the benefits of bidirectional tracing.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Emma J. Chory, Dana W. Gretton, Erika A. DeBenedictis, Kevin M. Esvelt
Summary: Researchers have developed Pyhamilton, an open-source Python platform for executing complex pipetting patterns required for high-throughput experiments. By integrating a plate reader, they were able to maintain nearly 500 remotely monitored bacterial cultures in log-phase growth without the need for user intervention. Using this technology, they successfully optimized bioreactor protein production and comprehensively sampled the carbon, nitrogen, and phosphorus fitness landscape.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Surojit Biswas, Grigory Khimulya, Ethan C. Alley, Kevin M. Esvelt, George M. Church
Summary: The approach introduced in this study utilizes machine learning to build accurate virtual fitness landscapes and screen millions of sequences via in silico directed evolution using minimal functionally assayed mutant sequences. This method not only helps in quickly identifying enhanced protein variants, but also efficiently utilizes resources for high-throughput screening.
Article
Biochemical Research Methods
Erika A. DeBenedictis, Emma J. Chory, Dana W. Gretton, Brian Wang, Stefan Golas, Kevin M. Esvelt
Summary: The PRANCE system allows for comprehensive exploration of biomolecular evolution by conducting high-throughput experiments on different types of biomolecules, revealing that evolution is influenced by both random chance and historical environmental changes. This system enhances the reliability of protein engineering and provides insight into how variables affect evolutionary outcomes.
Article
Biology
Erika Alden DeBenedictis, Dieter Soll, Kevin M. Esvelt
Summary: This study investigates the tolerance of the Escherichia coli genetic code to tRNA mutations and found that while most tRNAs can be converted to a quadruplet form, only nine aminoacyl tRNA synthetases can tolerate quadruplet anticodons. This limits the chemical alphabet available for an all-quadruplet code.
Article
Multidisciplinary Sciences
Andrew C. Payne, Zachary D. Chiang, Paul L. Reginato, Sarah M. Mangiameli, Evan M. Murray, Chun-Chen Yao, Styliani Markoulaki, Andrew S. Earl, Ajay S. Labade, Rudolf Jaenisch, George M. Church, Edward S. Boydenit, Jason D. Buenrostrot, Fei Chen
Summary: In situ genome sequencing (IGS) allows for sequencing and imaging of genomes within intact biological samples, providing spatial localization of genomic loci and revealing parent-specific changes in genome structure across embryonic stages, single-cell chromatin domains in zygotes, and epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate the capability of IGS to directly connect sequence and structure across length scales from single base pairs to whole organisms.
Letter
Oncology
Li Zhang, Lin Tian, Xiaoyang Dai, Hua Yu, Jiajia Wang, Anhua Lei, Mengmeng Zhu, Jianpo Xu, Wei Zhao, Yuqing Zhu, Zhen Sun, Hao Zhang, Yongxian Hu, Yanlin Wang, Yuming Xu, George M. Church, He Huang, Qinjie Weng, Jin Zhang
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2020)