Article
Biotechnology & Applied Microbiology
Chunwei Zheng, Shun-Qing Liang, Bin Liu, Pengpeng Liu, Suet-Yan Kwan, Scot A. Wolfe, Wen Xue
Summary: Prime editor (PE) has great potential for gene therapy, but it is challenging to deliver PE in vivo. In this study, a compact PE without the RNase H domain was developed, which showed comparable editing efficiency with full-length PE. Using a Cas9 split site, robust editing was achieved in both cells and mouse liver. Furthermore, the compact PE efficiently mediated gene insertion in mouse liver without the stop codon read-through effect observed with full-length PE, indicating its potential for advancing prime editing in vivo.
Review
Genetics & Heredity
Marta Stevanovic, Elena Piotter, Michelle E. McClements, Robert E. MacLaren
Summary: CRISPR/Cas gene editing is a revolutionary technology for correcting genetic mutations in vivo. AAV vectors are potential tools for delivering CRISPR/Cas, but their limited capacity is a restriction. Identifying smaller Cas orthologs that can be packaged into a single AAV would optimize gene editing and expand the targeted genetic sites.
CURRENT GENE THERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Jose Bonafont, Angeles Mencia, Esteban Chacon-Solano, Wai Srifa, Sriram Vaidyanathan, Rosa Romano, Marta Garcia, Rosario Hervas-Salcedo, Laura Ugalde, Blanca Duarte, Matthew H. Porteus, Marcela Del Rio, Fernando Larcher, Rodolfo Murillas
Summary: This study presents a gene-editing approach using CRISPR-Cas9 system to achieve gene correction in different cell types, showing therapeutic potential for RDEB.
Article
Medicine, Research & Experimental
Divya Ail, Duohao Ren, Elena Brazhnikova, Celine Nouvel-Jaillard, Stephane Bertin, Seyed Bagher Mirashrafi, Sylvain Fisson, Deniz Dalkara
Summary: This study investigates the potential inflammatory responses in AAV-mediated retinal gene therapy and the correlation between pre-existing serum antibodies and clinical outcomes. The results show a dose-dependent increase in antibodies after injection, and a correlation between serum antibody levels, inflammation, and transgene expression.
MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT
(2022)
Article
Immunology
Julie Brault, Taylor Liu, Siyuan Liu, Amanda Lawson, Uimook Choi, Nikita Kozhushko, Vera Bzhilyanskaya, Mara Pavel-Dinu, Ronald J. Meis, Michael A. Eckhaus, Sandra S. Burkett, Marita Bosticardo, Benjamin P. Kleinstiver, Luigi D. Notarangelo, Cicera R. Lazzarotto, Shengdar Q. Tsai, Xiaolin Wu, Gary A. Dahl, Matthew H. Porteus, Harry L. Malech, Suk See De Ravin
Summary: Ex vivo gene therapy has shown significant clinical benefits in treating Inborn errors of Immunity (IEIs) through the use of engineered retroviral vectors. However, concerns regarding potential genotoxicities have arisen due to random vector integrations. The targeted correction through CRISPR-Cas9-based genome editing offers improved precision and safety for functional correction of IEIs.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Immunology
Hildegund C. J. Ertl
Summary: Adeno-associated virus (AAV)-mediated gene transfer has shown benefits in treating patients with inherited diseases like hemophilia B, but challenges remain due to potential rejection of AAV-transduced cells. Immunosuppression may prevent rejection in some patients. CD8(+) T cells induced by AAV infections may recognize AAV vector's capsids and eliminate cells expressing degraded capsid antigens, or AAV vectors themselves may induce de novo T cell responses, particularly at high doses. This chapter discusses strategies to prevent activation of CD8(+) T cell responses to AAV infections and gene transfer.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Fisheries
Wan-Ping Bian, Shao-Lin Xie, Chao Wang, Grigoriy G. Martinovich, Yan-Bo Ma, Pan-Pan Jia, De-Sheng Pei
Summary: By generating a mitfa knock-out zebrafish line, the study reveals the impact of mitfa on the immune system, with reduced melanin levels and decreased macrophage numbers in mitfa-/- zebrafish. Interestingly, the expression levels of immune-related genes were significantly increased in mitfa-/- zebrafish after bacterial challenge or bifenazate exposure. Xenograft experiments showed a low cell migration ratio, indicating highly activated immune system after loss of mitfa.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Duohao Ren, Sylvain Fisson, Deniz Dalkara, Divya Ail
Summary: Inherited retinal diseases are a major cause of blindness, and gene therapy using gene editing techniques like CRISPR-Cas9 shows promise for their treatment. However, ocular gene therapies can elicit immune responses that need to be managed to ensure safe and effective gene editing.
Article
Biochemistry & Molecular Biology
Yi-Li Feng, Si-Cheng Liu, Ruo-Dan Chen, Xiu-Na Sun, Jing-Jing Xiao, Ji-Feng Xiang, An-Yong Xie
Summary: In CRISPR/Cas9 genome editing, dCas9 can be loaded onto a DSB-adjacent site to stimulate HDR and suppress c-NHEJ, providing a control over genome editing. This method can increase HDR-mediated CRISPR genome editing without exacerbating off-target effects.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, Research & Experimental
Thomas Kocher, Johannes Bischof, Simone Alexandra Haas, Oliver Patrick March, Bernadette Liemberger, Stefan Hainzl, Julia Illmer, Anna Hoog, Katharina Muigg, Heide-Marie Binder, Alfred Klausegger, Dirk Strunk, Johann Wolfgang Bauer, Toni Cathomen, Ulrich Koller
Summary: Gene editing through homology-directed repair (HDR) using Cas9 nuclease and nickase with donor templates has achieved correction efficiencies of up to 21% and 10% in primary RDEB keratinocytes and fibroblasts, leading to restoration of type VII collagen. The combination of paired nicking and single-stranded oligonucleotides proved to be a highly efficient COL7A1-editing strategy, with improved safety profile, representing a significant advancement in the field of traceless genome editing for genodermatoses.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Microbiology
Vaiva Gradauskaite, Marine Inglebert, John Doench, Melanie Scherer, Martina Dettwiler, Marianne Wyss, Neeta Shrestha, Sven Rottenberg, Philippe Plattet
Summary: Oncolytic viruses have gained attention as an alternative treatment for cancers. The Onderstepoort strain of canine distemper virus (CDV-OP), a safe and efficient vaccine for distemper in dogs, has shown promising oncolytic properties. By conducting a genome-wide CRISPR/Cas9 knockout screen, LRP6 was identified as a key receptor for CDV-OP entry in multiple cancer cell lines.
Article
Biochemistry & Molecular Biology
Xiaopeng Song, Yaxiong Cui, Yanxiao Wang, Yizhe Zhang, Qi He, Zhenyang Yu, Chengfang Xu, Huimin Ning, Yuying Han, Yunting Cai, Xuan Cheng, Jian Wang, Yan Teng, Xiao Yang, Jun Wang
Summary: In this study, the AAV-BR1-CRISPR system was used to specifically knock out target genes in brain endothelial cells of adult mice, demonstrating its effectiveness in rapidly identifying endothelial genes that regulate blood-brain barrier integrity in vivo.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Shengyao Zhi, Yuxi Chen, Guanglan Wu, Jinkun Wen, Jinni Wu, Qianyi Liu, Yang Li, Rui Kang, Sihui Hu, Jiahui Wang, Puping Liang, Junjiu Huang
Summary: Prime editor (PE) is a new genome editing tool that has the potential to correct the majority of known human genetic disease-related mutations. In this study, split-PEs were constructed and delivered using dual adenoassociated viruses (AAVs), successfully mediating gene editing in human cells and adult mouse retina.
Article
Oncology
Jason Yongsheng Chan, Grace Fangmin Tan, Joe Yeong, Chee Wee Ong, Dave Yong Xiang Ng, Elizabeth Lee, Joanna Koh, Cedric Chuan-Young Ng, Jing Yi Lee, Wei Liu, Ru Xin Wong, Chin-Ann Johnny Ong, Mohamad Farid, Bin Tean Teh, Khee Chee Soo
Summary: This study found a correlation between peripheral blood neutrophil-to-lymphocyte ratio (NLR) and intra-tumoral immune profiles in angiosarcomas, with higher NLR associated with worse overall survival. Additionally, high NLR was positively correlated with oncogenic pathway scores in the tumor microenvironment, suggesting a potential link between systemic and local immune responses and chemotherapy outcomes in these patients.
NPJ PRECISION ONCOLOGY
(2021)
Article
Clinical Neurology
Emrah Gumusgoz, Dikran R. Guisso, Sahba Kasiri, Jun Wu, Matthew Dear, Brandy Verhalen, Silvia Nitschke, Sharmistha Mitra, Felix Nitschke, Berge A. Minassian
Summary: Many adult and most childhood neurological diseases have a genetic basis, and CRISPR/Cas9 technology shows promise in treating them. By using CRISPR/Cas9 to disrupt gene sequences in adult polyglucosan body disease and Lafora disease mouse models, the researchers were able to reduce abnormal glycogen accumulation and improve neuroinflammatory markers, demonstrating the potential of this therapy for neurological diseases.
Article
Chemistry, Multidisciplinary
Rui Ye, Wei Song, Xinwen Ou, Zonglin Gu, Dong Zhang
Summary: Both fresh and aged two-dimensional molybdenum disulfide nanosheets can insert into lipid membranes, but the fresh nanosheets show stronger interaction and deeper penetration than the aged ones. The insertion of fresh MoS2 into lipid membranes is energetically favorable, and it can cause more damage to membrane integrity compared to the aged MoS2.
FRONTIERS IN CHEMISTRY
(2021)
Article
Cell Biology
Chady H. Hakim, Hsiao T. Yang, Matthew J. Burke, James Teixeira, Gregory J. Jenkins, N. Nora Yang, Gang Yao, Dongsheng Duan
Summary: By studying aged dystrophin-null canines' muscle pathology and contractile properties, we established a foundation for using this model in research on experimental therapies for Duchenne muscular dystrophy, revealing an unexpected myofiber-type switch in affected dogs.
DISEASE MODELS & MECHANISMS
(2021)
Article
Biotechnology & Applied Microbiology
Nalinda B. Wasala, Emily D. Million, Thais B. Watkins, Lakmini P. Wasala, Jin Han, Yongping Yue, Baisong Lu, Shi-jie Chen, Chady H. Hakim, Dongsheng Duan
Summary: Short-term local injection of CRISPR editing technique can restore dystrophin in DMD patients, while long-term systemic injection failed. The study found that long-term systemic injection resulted in selective loss of gRNA vector, which was not affected by the injection time and dosage. In addition, a higher dose of gRNA vector was associated with better therapeutic effects.
HUMAN GENE THERAPY
(2022)
Article
Polymer Science
Ke Li, Jiaxin Wu, Fuchen Guo, Yaxin Wang, Dong Zhang, Linxi Zhang
Summary: This study investigates the sliding dynamics of a ring chain on a fixed block copolymer using molecular dynamics simulations and the Lifson-Jackson formula. The study reveals that the sliding dynamics strongly depend on the block length, A-block volume fraction, and block-ring interaction strength. The width and height of the free energy potential well and barrier determine the sliding diffusion behavior. The findings are in good agreement with theoretical analysis and offer insights into diffusion in periodic media.
Article
Multidisciplinary Sciences
Xiqiao Zhang, Gregory J. Jenkins, Chady H. Hakim, Dongsheng Duan, Gang Yao
Summary: This study developed a 4-limb canine gait analysis system using wireless inertial measurement units (IMUs) and evaluated its accuracy compared to a pressure-sensor based walkway gait system. The results showed a high correlation between the stride parameters measured in both systems. The 4-limb system successfully visualized the overall gait types and identified rapid gait changes in dogs.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Jun Li, Sicheng Zhang, Dong Zhang, Shi-Jie Chen
Summary: RNA 3D structures play a crucial role in understanding their functions and designing drugs targeting RNA. However, experimentally determining RNA 3D structures is labor-intensive and technically challenging, resulting in a significant gap between the number of sequences and the availability of RNA structures. Therefore, computer-aided prediction of RNA 3D structures from sequences has become a highly desirable solution. In this study, a pipeline server integrating Vfold2D, Vfold3D, and VfoldLA programs is presented, enabling efficient and accurate prediction of RNA 3D structures or reliable initial structures for further refinement using an expanded 3D template database and 2D structural constraints extracted from the Rfam database.
Article
Biochemistry & Molecular Biology
Julita Gumna, Maciej Antczak, Ryszard W. Adamiak, Janusz M. Bujnicki, Shi-Jie Chen, Feng Ding, Pritha Ghosh, Jun Li, Sunandan Mukherjee, Chandran Nithin, Katarzyna Pachulska-Wieczorek, Almudena Ponce-Salvatierra, Mariusz Popenda, Joanna Sarzynska, Tomasz Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Zok, Eric Westhof, Zhichao Miao, Marta Szachniuk, Agnieszka Rybarczyk
Summary: RNA is a unique biomolecule, and computational 3D structure prediction methods are rapidly developing. We introduced a computational pipeline for comparative analysis of 3D RNA structures and demonstrated its application in the RNA-Puzzles challenge.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Deyin Wang, Xiaohui Wen, Dong Zhang, Jiajun Tang
Summary: In this study, the effect of arms and shear flow on the dynamical and structural properties of the comb long-chain branched (LCB) polymer with dense arms was investigated using hybrid multi-particle collision dynamics (MPCD) and molecular dynamics (MD) methods. The results show that the LCB polymer undergoes periodic stretched-folded-stretched state transition and rotation, with the arms playing a role in stabilizing the polymer's motion. The impact induced by random and fast motions of arms and backbone decreases as the shear rate increases. The length of the arms and the conformational distribution are found to be important factors affecting the rotation period of the LCB polymer. The structural properties analysis reveals that the changes in gyration of the LCB polymer are in accordance with its rolling behavior, and the resistance to configuration expansion against the imposed flow field is stronger for the comb polymer with shorter arms. Additionally, with increasing arm length, the comb polymer transitions from linear-polymer-like to capsule-like behavior in shear flow.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Deyin Wang, Xiaohui Wen, Dong Zhang, Xinguan Tan, Jiajun Tang
Summary: The stretching dynamics and dynamical behaviors of individual branched ring polymer (BRP) were studied in steady shear flow. The nonmonotonic increase of polymer size with increasing branch length was observed. A universal power law described the decrease of alignment angle during the first downward phase. Tumbling and tank-treading motions were reflected by periodic and non-periodic changes of the polymer's ring backbone.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Cardiac & Cardiovascular Systems
Emily D. D. Morales, Yongping Yue, Thais B. B. Watkins, Jin Han, Xiufang Pan, Aaron M. M. Gibson, Bryan Hu, Omar Brito-Estrada, Gang Yao, Catherine A. A. Makarewich, Gopal J. J. Babu, Dongsheng Duan
Summary: This study identified DWORF as a potential therapeutic target for Duchenne muscular dystrophy (DMD) cardiomyopathy. Gene therapy using adeno-associated virus serotype 9-DWORF vector significantly enhanced SERCA activity, reduced myocardial fibrosis, and improved exercise capacity, cardiac function, and hemodynamics in mdx mice. These findings suggest that DWORF gene therapy holds promise for treating DMD cardiomyopathy.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Yue Qiu, Hongyang Wang, Huaye Pan, Jing Guan, Lei Yan, Mingjie Fan, Hui Zhou, Xuanhao Zhou, Kaiwen Wu, Zexiao Jia, Qianqian Zhuang, Zhaoying Lei, Mengyao Li, Xue Ding, Aifu Lin, Yong Fu, Dong Zhang, Qiuju Wang, Qingfeng Yan
Summary: Auditory neuropathy spectrum disorder (ANSD) is a type of sensorineural deafness characterized by abnormal inner hair cells and/or auditory nerve function, while outer hair cell function remains intact. Through analysis and experiments, it is found that mutations in the apoptosis-inducing factor mitochondria-associated 1 (AIFM1) impair dimerization and compromise AIF function, resulting in caspase-independent apoptosis, which contributes to ANSD. Furthermore, nicotinamide adenine dinucleotide (NADH) treatment has shown potential as a drug for ANSD treatment by rescuing AIF dimerization and reducing apoptosis.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2023)
Article
Chemistry, Physical
Linlin Tang, Mengjiao Huang, Mingjiao Zhang, Yufeng Pei, Yan Liu, Yong Wei, Chaoyong Yang, Teng Xie, Dong Zhang, Ruhong Zhou, Yanling Song, Jie Song
Summary: Multivalent interactions enhance the binding efficiency of ligands to target molecules. A direct SELEX strategy using a preorganized DNA framework library was developed to select an antibody-mimicking multivalent aptamer (Amap) for epithelial cell adhesion molecule (EpCAM). Amap exhibits good binding affinity through both aptamer moieties binding to EpCAM simultaneously, and this strategy has the potential to be a new route for de novo evolution of multivalent aptamers.
Article
Multidisciplinary Sciences
Dong Zhang, Lulu Qiao, Xiaobo Lei, Xiaojing Dong, Yunguang Tong, Jianwei Wang, Zhiye Wang, Ruhong Zhou
Summary: In this study, the binding interface between the SARS-CoV-2 stem-loop 3 (SL3) cis-acting element and human TIA1 protein was characterized using a combined theoretical and experimental approach. The highly structured SARS-CoV-2 SL3 exhibited a strong binding affinity to TIA1 protein, with the specific binding being directed by aromatic stacking, hydrogen bonds, and hydrophobic interactions. Mutagenesis studies confirmed the proposed 3D binding model and identified SL3 variants with enhanced binding affinities to TIA1. Blocking the RNA-protein interactions with designed antisense oligonucleotides significantly reduced SARS-CoV-2 infection in cells. Additionally, TIA1 protein was found to interact with conserved SL3 RNA elements in other betacoronavirus lineages.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Qianqian Zhuang, Fengfeng Guo, Lei Fu, Yufei Dong, Shaofang Xie, Xue Ding, Shuangyi Hu, Xuanhao D. Zhou, Yangwei Jiang, Hui Zhou, Yue Qiu, Zhaoying Lei, Mengyao Li, Huajian Cai, Mingjie Fan, Lingjie Sang, Yong Fu, Dong Zhang, Aifu Lin, Xu Li, Tilo Kunath, Ruhong Zhou, Ping Liang, Zhong Liu, Qingfeng Yan
Summary: Hypertrophic cardiomyopathy (HCM) is a leading cause of sudden cardiac death in young individuals. In this study, a compound called 1-Deoxynojirimycin (DNJ) was found to rescue mitochondrial function in HCM cells by promoting the oligomerization of optic atrophy protein 1 (OPA1) and reconstructing the mitochondrial cristae. DNJ also improved the physiological properties of HCM cells and alleviated cardiac hypertrophy in a mouse model. These findings provide insights into the mechanism of HCM and offer a potential therapeutic strategy.
JOURNAL OF CLINICAL INVESTIGATION
(2023)