Article
Oncology
Elyse C. C. Page, Susan L. L. Heatley, Jacqueline Rehn, Paul Q. Q. Thomas, David T. T. Yeung, Deborah L. L. White
Summary: ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) PATIENTS WITH GAIN OF CHROMOSOME 21, INTRACHROMOSOMAL AMPLIFICATION OF CHROMOSOME 21 (IAMP21), OR DOWN SYNDROME (DS) HAVE INCREASED EXPRESSION OF GENES IN THE DS CRITICAL REGION (DSCR) OF CHROMOSOME 21, INCLUDING HMGN1. A DELETION IN THE PSEUDOAUTOSOMAL REGION OF THE X/Y CHROMOSOME RESULTING IN P2RY8::CRLF2 GENE FUSION IS COMMON IN DS-ALL AND IAMP21 PATIENTS. THIS STUDY DEMONSTRATES THAT HMGN1 INCREASES THE PROPENSITY FOR P2RY8::CRLF2 DEVELOPMENT, WITH IMPLICATIONS FOR PATIENTS WITH DS, +21, OR IAMP21.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Xiaoying Zhao, Kunli Qu, Benedetta Curci, Huanming Yang, Lars Bolund, Lin Lin, Yonglun Luo
Summary: Recent progress in CRISPR gene editing tools has expanded the possibilities for treating devastating genetic diseases. In this study, three methods of gene editing (NHBEJ, HDR, and PE) were compared for correcting loss-of-function mutations in Duchenne Muscular Dystrophy. The highest efficiency was achieved with NHBEJ, followed by HDR and PE2. The correction efficiency was increased with the use of PE3. This study demonstrates the potential for highly efficient correction of DMD mutations using CRISPR gene editing.
Article
Chemistry, Multidisciplinary
Qian Ban, Peng Yang, Shih-Jie Chou, Li Qiao, Haidong Xia, Jingjing Xue, Fang Wang, Xiaobin Xu, Na Sun, Ryan Y. Zhang, Ceng Zhang, Athena Lee, Wenfei Liu, Ting-Yi Lin, Yu-Ling Ko, Petar Antovski, Xinyue Zhang, Shih-Hwa Chiou, Chin-Fa Lee, Wenqiao Hui, Dahai Liu, Steven J. Jonas, Paul S. Weiss, Hsian-Rong Tseng
Summary: CRISPR/Cas9 technology offers a versatile solution for treating genetic diseases through efficient and precise gene editing. A nonviral delivery strategy involving encapsulating Cas9·sgRNA ribonucleoprotein complexes into supramolecular nanoparticles has shown promise in targeted cell delivery, demonstrating efficient gene disruption in various cell types.
Review
Virology
Man Teng, Yongxiu Yao, Venugopal Nair, Jun Luo
Summary: CRISPR/Cas9-based gene-editing techniques have been widely applied in biological sciences, particularly in modifying viral genomes, to reveal gene function, virus pathogenesis, and play a crucial role in vaccine development.
Article
Horticulture
Wenxue Cao, Xin Dong, Jialei Ji, Limei Yang, Zhiyuan Fang, Mu Zhuang, Yangyong Zhang, Honghao Lv, Yong Wang, Peitian Sun, Yumei Liu, Zhansheng Li, Fengqing Han
Summary: BoCER1 was found to be expressed in all cabbage tissues except roots, and its function in cabbage was determined using CRISPR technology. Creating wax-less cabbage through gene editing may aid in breeding brilliant green cabbage varieties.
SCIENTIA HORTICULTURAE
(2021)
Review
Biochemistry & Molecular Biology
Hua Liu, Wendan Chen, Yushu Li, Lei Sun, Yuhong Chai, Haixia Chen, Haochen Nie, Conglin Huang
Summary: The rapid growth of the global population has increased the demand for food crops significantly. Traditional crop breeding methods cannot meet the future global food demand. New gene-editing technologies, especially CRISPR/Cas9, can rapidly improve crop traits and create new germplasm materials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Agronomy
Xingdan Liu, Qi Ding, Wenshu Wang, Yanling Pan, Chao Tan, Yingbo Qiu, Ya Chen, Hongjing Li, Yinlong Li, Naizhong Ye, Nian Xu, Xiao Wu, Rongjian Ye, Jianfeng Liu, Chonglie Ma
Summary: This study presents a novel strategy to increase amylose content in rice by using CRISPR/Cas9 technology to delete the first intron of the Wx gene. It was found that the deletion of the first intron significantly increased the amylose content in rice carrying the Wx(b) allele. Furthermore, it was observed that the first intron of the Wx gene mainly regulates Wx gene expression at the post-transcriptional level.
Article
Biochemistry & Molecular Biology
Xi Chen, Xuran Niu, Yang Liu, Rui Zheng, Lei Yang, Jian Lu, Shuming Yin, Yu Wei, Jiahao Pan, Ahmed Sayed, Xueyun Ma, Meizhen Liu, Fengxiang Jing, Mingyao Liu, Jiazhi Hu, Liren Wang, Dali Li
Summary: This study demonstrates the successful application of the HITI strategy for targeted gene integration in a hemophilia B rat model, leading to significant improvement in hemophilia symptoms over a nine-month period.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Biochemical Research Methods
Meliawati Meliawati, Christa Teckentrup, Jochen Schmid
Summary: The CRISPR-Cas system has been used for large cluster deletion and multiplex genome editing in Paenibacillus polymyxa. The study demonstrates that the Cas9-based system can achieve efficient targeted deletions and multiplex editing, which is expected to accelerate future research in P. polymyxa and related species.
ACS SYNTHETIC BIOLOGY
(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
Biotechnology & Applied Microbiology
Guoliang Meng, Xuping Wang, Mengqian Liu, Fen Wang, Qizheng Liu, Caihong Dong
Summary: In this study, an efficient CRISPR/Cas9 genome-editing system was successfully constructed in Cordyceps militaris, allowing for gene editing and precise gene deletion with high efficiencies. The findings demonstrate the potential of plasmid loss in avoiding adverse effects of the CRISPR/Cas9 system and facilitating the breeding of new cultivars. Additionally, RNA Pol III promoters, endogenous tRNA, and chimeric tRNA can be used to improve editing efficiency.
MICROBIAL BIOTECHNOLOGY
(2022)
Review
Agronomy
Xuehan Xia, Xinhua Cheng, Rui Li, Juanni Yao, Zhengguo Li, Yulin Cheng
Summary: Genome editing, represented by the CRISPR/Cas9 system, has been widely used in plants for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and customizing tomato cultivars for urban agriculture. Tomato, as an important applied plant, serves as an excellent model plant for genome editing research.
THEORETICAL AND APPLIED GENETICS
(2021)
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)
Article
Cell Biology
Farzaneh Alizadeh, Yousef Jafari Abraghan, Shima Farrokhi, Yasamin Yousefi, Yeganeh Mirahmadi, Atieh Eslahi, Majid Mojarrad
Summary: In this study, four immortalized DMD muscle cell lines were successfully created using an optimized CRISPR/Cas9 gene editing approach, demonstrating the efficacy of the CRISPR-Cas9 system in generating DMD cell models with targeted deletions.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Hang Yuan, Qi Kang, Zhehui Li, Xuanxuan Bai, Jianxin Jia, Daxiong Han, Xijie Wu, Mingyu Li
Summary: Glucagon receptor antagonism is a potential effective treatment for diabetes, but its functions have not been fully elucidated. Using Crispr-Cas9 technique, researchers generated a novel allele of GCGR in mice that completely lacks GCGR protein. Complete deletion of Gcgr leads to hyperglucagonemia, α-cell hyperplasia, and improvement of glucose tolerance, similar to Gcgr-truncated mutation in mice. This novel GCGR knockout mouse strain provides a valuable tool for studying GCGR function.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Barbora Salovska, Wenxue Li, Yi Di, Yansheng Liu
Summary: The latest high-resolution, high-speed mass spectrometers with data-independent acquisition (DIA) provide a powerful analytical tool for biological investigations. The optimized high-selectivity DIA-MS named BoxCarmax significantly improves quantitative accuracy in complex samples, such as SILAC and pSILAC, by mitigating ratio suppression of isotope-peptide pairs. The BoxCarmax approach offers an alternative and accurate method for analyzing protein turnover and complex samples.
ANALYTICAL CHEMISTRY
(2021)
Article
Cell Biology
Evanthia Pangou, Olga Bielska, Lucile Guerber, Stephane Schmucker, Arantxa Agote-Aran, Taozhi Ye, Yongrong Liao, Marta Puig-Gamez, Erwan Grandgirard, Charlotte Kleiss, Yansheng Liu, Emmanuel Compe, Zhirong Zhang, Ruedi Aebersold, Romeo Ricci, Izabela Sumara
Summary: This study reveals a pathway linking mitochondrial fission to mitotic progression in mammalian cells, showing that PKD/MFF-dependent mitochondrial fission is essential for chromosome segregation and cell survival during cell division.
Article
Chemistry, Analytical
Clinton Yu, Xiaorong Wang, Wenxue Li, Yansheng Liu, Lan Huang
Summary: The 26S proteasome is responsible for intracellular degradation in eukaryotes and is composed of two subcomplexes, the 20S core particle and the 19S regulatory particle. A bimolecular affinity purification method using dual-baits has been developed to improve the homogeneity of resulting proteasome complexes. The strategy has been shown to be effective in facilitating detailed assessments of complex-specific molecular details and can be applied to studying other complexes.
ANALYTICAL CHEMISTRY
(2021)
Article
Materials Science, Ceramics
Junwei Hou, Bingxuan Huang, Lingcong Kong, Yu Xie, Yansheng Liu, Mengmeng Chen, Qingyao Wang
Summary: TiO2 nanotube arrays (TiO2 NTs) were modified with CdS-CuS co-sensitizers to enhance photocatalytic performance and stability. The suitable composition of CdS-CuS showed improved pollutant removal and photocurrent/H-2 generation, indicating potential for environmental remediation and new energy development.
CERAMICS INTERNATIONAL
(2021)
Article
Biochemical Research Methods
Yansheng Liu
Summary: Protein post-translational modifications (PTMs) play a crucial role in generating diverse proteoforms, yet current studies mainly focus on PTM site-specific rather than proteoform-specific approaches. The suggested matching strategy between modified and unmodified peptidoforms could offer more relevant information for understanding PTM site-specific biological functions. The use of peptidoform nomenclature is advocated for future bottom-up proteomic studies.
Article
Cell Biology
Jaekwang Jeong, Jae Hun Shin, Wenxue Li, Jun Young Hong, Jaechul Lim, Jae Yeon Hwang, Jean-Ju Chung, Qin Yan, Yansheng Liu, Jungmin Choi, John Wysolmerski
Summary: The lipid raft resident protein MAL2 contributes to the pathogenesis of malignancies, including breast cancer, through its effects on HER2 signaling and membrane stability. Physical interactions between HER2 and MAL2 in lipid rafts play a key role in maintaining low intracellular calcium concentrations and are enhanced in trastuzumab-resistant breast cancer cells, suggesting MAL2 as a potential therapeutic target.
Article
Multidisciplinary Sciences
Qian Ba, Yuanyuan Hei, Anasuya Dighe, Wenxue Li, Jamie Maziarz, Irene Pak, Shisheng Wang, Gunter P. Wagner, Yansheng Liu
Summary: This study quantified proteomic and phosphoproteomic layers in fibroblasts from 11 common mammalian species and found that transcript and protein expression levels follow functional role and exhibit coevolution. Gene expression variability is universal but varies between individuals and species, with RNA metabolic processes showing higher interspecies variation. The ubiquitin-proteasome system is conserved in mammals, while lysosome-mediated protein degradation varies between mammalian lineages. Phosphosite profiles reveal a phosphorylation coevolution network independent of protein abundance.
Article
Biochemical Research Methods
Wenxue Li, Barbora Salovska, Eugenio F. F. Fornasiero, Yansheng Liu
Summary: Recent studies have integrated post-translational modifications (PTMs) measurement with protein turnover exploration in steady state systems. However, the biological interpretation of these complex datasets remains unclear.
Article
Chemistry, Multidisciplinary
Zhenyi Hu, Po-Han Chen, Wenxue Li, Todd Douglas, John Hines, Yansheng Liu, Craig M. Crews
Summary: Microtubule-associated protein tau is crucial for microtubule assembly and stabilization. Tau hyperphosphorylation is implicated in the development of Alzheimer's disease and tauopathies. In this study, we used small molecule-based PhosTACs to induce efficient and sustained tau dephosphorylation by recruiting tau to PP2A, a native tau phosphatase. Mass spectrometry data validated that PhosTACs downregulated multiple phosphorylation sites of tau. Our findings suggest that PhosTACs represent a potential avenue for disease-modifying therapies for tauopathies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Editorial Material
Biochemical Research Methods
Barbora Salovska, Yansheng Liu
Article
Multidisciplinary Sciences
Marcelo Perez-Pepe, Anthony W. Desotell, Hengyi Li, Wenxue Li, Bing Han, Qishan Lin, Daryl E. Klein, Yansheng Liu, Hani Goodarzi, Claudio R. Alarcon
Summary: A fundamental feature of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. We found that epidermal growth factor signaling induces phosphorylation of the enzyme methyltransferase 3 (METTL3), leading to METTL3-mediated methylation of 7SK. 7SK methylation enhances its binding to heterogeneous nuclear ribonucleoproteins, causing the release of the HEXIM1/P-TEFb complex and inducing transcriptional elongation. Our findings establish the mechanism underlying 7SK activation and uncover a previously unknown function for the m6A modification in converting growth factor signaling events into a regulatory transcriptional response via an RNA methylation-dependent switch.
Article
Oncology
Barbora Salovska, Erli Gao, Sophia Mueller-Dott, Li Wenxue, Carlos Chacon Cordon, Wang Shisheng, Aurelien Dugourd, George Rosenberger, Julio Saez-Rodriguez, Liu Yansheng
Summary: This study found that long-term use of the oral antidiabetic drug metformin can significantly alter the signaling network of colorectal cancer cells. Through network analysis and metabolite labeling, the study also identified candidate drugs with potential anticancer effects. This research provides an important resource for understanding the mechanism of metformin-induced cell signaling.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Xiaoxiang Huang, Ziao Gan, Haowei Cui, Tian Lan, Yansheng Liu, Etienne Caron, Wenguang Shao
Summary: SysteMHC Atlas v2.0 is a comprehensive mass spectrometry-based immunopeptidomics database, providing a large collection of MHC-bound peptides and modified peptides. It introduces new features and tools, and offers various resources for data mining and immunopeptidomic analysis. This database provides important insights for the immunology and proteomics community.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Yansheng Liu, Wenxue Li, Qian Ba, Anatoly Kiyatkin, Archer Hamidzadeh, Eugenio Fornasiero, Barbora Salovska
Article
Biochemistry & Molecular Biology
Erli Gao, Wenxue Li, Chongde Wu, Wenguang Shao, Yi Di, Yansheng Liu
Summary: This study used a DIA-MS method to measure proteome and phosphoproteome of melanoma cell lines with different metastatic properties, demonstrating its potential for improving research reproducibility. The data confirmed mRNA-protein and protein-phosphosite correlations and identified altered phosphoprotein modules in metastatic cells. DIA-MS was established as a competitive proteotyping approach and provided valuable insights into metastatic proteotypes in melanoma cells.
