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.
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.
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)
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)
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
Min Ho Lee, Jae Il Shin, Jae Won Yang, Keum Hwa Lee, Do Hyeon Cha, Jun Beom Hong, Yeoeun Park, Eugene Choi, Kalthoum Tizaoui, Ai Koyanagi, Louis Jacob, Seoyeon Park, Ji Hong Kim, Lee Smith
Summary: This review highlights the current and potential use of CRISPR-Cas9 in the management of autoimmune diseases. Several studies have shown that CRISPR-Cas9 can be utilized for immunomodulation, reducing cholesterol, and treating rare diseases. However, there is limited research on the treatment of autoimmune diseases using CRISPR-Cas9.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Kristina J. Tatiossian, Robert D. E. Clark, Chun Huang, Matthew E. Thornton, Brendan H. Grubbs, Paula M. Cannon
Summary: This study found that CRISPR-Cas9 indel signatures can be used to identify gRNAs that maximize HDR outcomes, with the frequency of deletions resulting from MMEJ repair of at least 3 base pairs better predicts HDR frequency. Existing tools can be repurposed to identify gRNAs that promote HDR.
Article
Plant Sciences
Syed Inzimam Ul Haq, Dianfeng Zheng, Naijie Feng, Xingyu Jiang, Feng Qiao, Jin-Sheng He, Quan-Sheng Qiu
Summary: This review summarizes the advances of CRISPR/Cas9 technology in plant genome editing and discusses its applications in forage breeding, as well as the potential and challenges.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Juhee Lee, Yoo Kyung Kang, Eonju Oh, Juhee Jeong, San Hae Im, Duk Ki Kim, Haeshin Lee, Sang-Gyu Kim, Keehoon Jung, Hyun Jung Chung
Summary: The study presents a cancer gene therapy strategy based on NanoRNP that efficiently blocks the PD-L1 immune checkpoint and induces an antitumor effect in vivo without the need for combination therapy. In vivo results demonstrate that NanoRNP can induce indels in target cells at high frequencies, significantly suppressing tumor growth.
CHEMISTRY OF MATERIALS
(2022)
Article
Multidisciplinary Sciences
Beate Rieblinger, Hicham Sid, Denise Duda, Tarik Bozoglu, Romina Klinger, Antonina Schlickenrieder, Kamila Lengyel, Krzysztof Flisikowski, Tatiana Flisikowska, Nina Simm, Alessandro Grodziecki, Carolin Perleberg, Andrea Bahr, Lucie Carrier, Mayuko Kurome, Valeri Zakhartchenko, Barbara Kessler, Eckhard Wolf, Lutz Kettler, Harald Luksch, Ibrahim T. Hagag, Daniel Wise, Jim Kaufman, Benedikt B. Kaufer, Christian Kupatt, Angelika Schnieke, Benjamin Schusser
Summary: Research on genetically modified animals has mostly focused on mice, but also includes species like pigs that are more physiologically similar to humans, and cross-species comparisons with phylogenetically distant species like chickens. CRISPR-Cas9 is a versatile genetic editing method applicable across various species. The successful generation of transgenic chickens and pigs that express Cas9 in all organs has confirmed the functionality of Cas9 across different target genes, cell types, and in vivo applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Chao Zhang, Shanhe Liu, Xuan Li, Ruixuan Zhang, Jun Li
Summary: CRISPR/Cas-based genome editing technologies have revolutionized plant science by allowing precise manipulation of plant genomes. Virus-induced genome editing (VIGE) has emerged as a powerful method for delivering CRISPR/Cas reagents into plant cells, with high editing efficiency and simplified process. This article provides an overview of CRISPR/Cas-based genome editing and focuses on the VIGE systems, types of viruses used for CRISPR/Cas9 cassette delivery, recent applications, and challenges and potential of VIGE in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Chin-Kai Chuang, Wei-Ming Lin
Summary: Cas9-sgRNA is a key tool for genome editing, with its simplicity, unique RNA-guided DNA recognition activity, and independent nuclease activities. Different variants of Cas9, in combination with sgRNA, can achieve various effects on target site breakage. Additionally, engineered enzyme activities can be introduced using Cas9 derivatives, and methods for transient expression and biosafety have been developed to address off-target effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Peng Yang, Athena Yue-Tung Lee, Jingjing Xue, Shih-Jie Chou, Calvin Lee, Patrick Tseng, Tiffany X. Zhang, Yazhen Zhu, Junseok Lee, Shih-Hwa Chiou, Hsian-Rong Tseng
Summary: The CRISPR/Cas9 genome editing system has revolutionized the field of therapeutic applications for genetic diseases and cancers. Efficient delivery of the system in vivo remains a significant challenge. Non-viral nano-vectors offer advantages over viral vectors and can be used to deliver CRISPR/Cas9 cargoes for targeted gene editing. The article highlights recent advances in nano-vector delivery for treating cancers and genetic diseases and proposes strategies for future development.
Article
Veterinary Sciences
Zhi-Wei Zhang, Ting-Ting Li, Jin-Lei Wang, Qin-Li Liang, Hai-Sheng Zhang, Li-Xiu Sun, Xing-Quan Zhu
Summary: This study investigated the functions of two thioredoxins in T. gondii tachyzoites and found that their deletion did not affect important characteristics such as replication, egress, plaque formation, resistance to H2O2, and maintenance of ROS level and T-AOC in the RH strain. These thioredoxins may not be essential for the RH strain but may have roles in other strains of T. gondii.
FRONTIERS IN VETERINARY SCIENCE
(2021)
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)
Article
Multidisciplinary Sciences
Clare R. Harding, Matthew Gow, Joon Ho Kang, Emily Shortt, Scott R. Manalis, Markus Meissner, Sebastian Lourido
NATURE COMMUNICATIONS
(2019)
Editorial Material
Parasitology
Sebastian Lourido
TRENDS IN PARASITOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. Saeij, Alex K. Shalek, Sebastian Lourido
Article
Biochemistry & Molecular Biology
Alice L. Herneisen, Saima M. Sidik, Benedikt M. Markus, David H. Drewry, William J. Zuercher, Sebastian Lourido
ACS CHEMICAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Yifan Wang, Lamba Omar Sangare, Tatiana C. Paredes-Santos, Musa A. Hassan, Shruthi Krishnamurthy, Anna M. Furuta, Benedikt M. Markus, Sebastian Lourido, Jeroen P. J. Saeij
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Clare R. Harding, Saima M. Sidik, Boryana Petrova, Nina F. Gnaedig, John Okombo, Alice L. Herneisen, Kurt E. Ward, Benedikt M. Markus, Elizabeth A. Boydston, David A. Fidock, Sebastian Lourido
NATURE COMMUNICATIONS
(2020)
Article
Immunology
Benedikt M. Markus, Benjamin S. Waldman, Hernan A. Lorenzi, Sebastian Lourido
Summary: The study reveals that Toxoplasma produces specific transcription start sites at different stages, leading to the generation of mRNA isoforms with distinct 5' termini. Additionally, there is pervasive divergent transcription and nucleosome occupancy around promoters, highlighting the chromatin contributions to transcription initiation. A precise TSS map can uncover motifs associated with transcription initiation and provide a critical resource for functional genomics in Toxoplasma.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Benedikt M. Markus, Elizabeth A. Boydston, Sebastian Lourido
Summary: The study demonstrates the feasibility of CRISPR-mediated transcriptional regulation in Toxoplasma, showcasing the efficacy of dCas9 from Streptococcus pyogenes and Streptococcus thermophilus in generating intermediate levels of gene expression with durable repression. The distinct sgRNA scaffold requirements of the two dCas9s enable their orthogonal use for simultaneous examination of two distinct loci through transcriptional modulation, presenting a promising tool for functional characterization of the Toxoplasma genome.
Article
Microbiology
Tyler A. Smith, Gabriella S. Lopez-Perez, Alice L. Herneisen, Emily Shortt, Sebastian Lourido
Summary: A high-throughput tagging platform was developed to screen kinases in the parasite Toxoplasma gondii. It led to the discovery of a kinase named SPARK, which plays a crucial role in invasion and egress of the parasite. Despite homology to mammalian kinase PDK1, SPARK lacks a lipid-binding domain, suggesting a rewiring of the pathway in parasites. This high-throughput platform provides a scalable and versatile method for dissecting parasite biology.
NATURE MICROBIOLOGY
(2022)
Article
Biology
Alice L. Herneisen, Zhu-Hong Li, Alex W. Chan, Silvia N. J. Moreno, Sebastian Lourido
Summary: Apicomplexan parasites utilize Ca2+ signaling pathways to regulate specific cellular processes and contribute to the pathogenesis. Mapping the Ca2+-responsive proteome of Taxoplasma gondii revealed novel proteins involved in the signaling network and identified the Ca2+-responsive enzyme PP1 as a regulator of parasite motility.
Article
Biochemistry & Molecular Biology
Dylan Valleau, Saima M. Sidik, Luiz C. Godoy, Yamilex Acevedo-Sanchez, Charisse Flerida A. Pasaje, My-Hang Huynh, Vern B. Carruthers, Jacquin C. Niles, Sebastian Lourido
Summary: The microneme protein CLAMP, along with the invasion-associated SPATR and a previously uncharacterized protein CLAMP-linked invasion protein (CLIP), forms a complex that is essential for rhoptry discharge following host-cell contact. Phylogenetic analysis suggests that the essential complex components are present across apicomplexans.
Review
Microbiology
Dominic Schwarz, Sebastian Lourido
Summary: This paper discusses the important roles of apicomplexan parasites as transcription factors and chromatin regulators, with a focus on Myb domain-containing proteins. Through phylogenetic analysis, it reveals the diversity and regulatory mechanisms of Myb domain-containing proteins, highlighting their functional heterogeneity in parasite differentiation.
CURRENT OPINION IN MICROBIOLOGY
(2023)