Review
Chemistry, Physical
Weiran Su, Junru Li, Chen Ji, Congshuo Chen, Yuzheng Wang, Huili Dai, Fengqin Li, Peifeng Liu
Summary: CRISPR/Cas systems are powerful tools for disease biomarkers detection, capable of detecting nucleic acid and non-nucleic acid targets. This review summarizes the principles and characteristics of various CRISPR/Cas systems, and introduces the applications of CRISPR/Cas systems in detecting nucleic and non-nucleic acid targets. The prospects and challenges of their applications in biosensing are also discussed.
Review
Chemistry, Analytical
Yuxin Zhang, Yunping Wu, Yanfang Wu, Yangyang Chang, Meng Liu
Summary: The increasing demand for developing biosensors in various fields poses challenges on sensor performance requirements such as sensitivity, selectivity, and operating costs. CRISPR-Cas systems, known as molecular scissors, are highly accurate in cleaving specific DNA and RNA sequences, and recent studies have shown the establishment of versatile biosensing platforms based on CRISPR-Cas. The review introduces the general characteristics and mechanisms of class II CRISPR-Cas systems, highlighting their biosensing strategies for detecting a wide range of nucleic acid and non-nucleic acid analytes.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Siyu Chen, Bo Gong, Cong Zhu, Chunyang Lei, Zhou Nie
Summary: Nucleic acid molecules possess attractive properties for biosensing and bioimaging due to their high designability and structural predictability. CRISPR-Cas systems, with high programmability and flexibility, recognize and cleave nucleic acid targets and have been engineered as multifunctional tools. Integration of nucleic acids with CRISPR-Cas systems has advanced biosensing and bioimaging methodologies, holding great promise in biochemical research and clinical diagnosis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Pooja Bhardwaj, Rajni Kant, Sthita Pragnya Behera, Gaurav Raj Dwivedi, Rajeev Singh
Summary: This article emphasizes the importance of CRISPR/Cas technology as a diagnostic tool for early management, diagnosis, and treatment of infections and diseases, and explores its detection capabilities for non-nucleic acid targets as well as the technical challenges and improvements in clinical assessment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Medicine, General & Internal
Junwei Li, Yuexia Wang, Bin Wang, Juan Lou, Peng Ni, Yuefei Jin, Shuaiyin Chen, Guangcai Duan, Rongguang Zhang
Summary: The CRISPR/Cas system is an immune system that defends against foreign genetic attacks with its excellent target-specific sequence recognition ability. It has shown great performance in the development of pathogen nucleic acid detection technology. Researchers have made rapid, convenient, and feasible innovations in pathogen nucleic acid detection technology by combining it with various biosensing technologies. The development of CRISPR/Cas system is not limited to CRISPR/Cas9 and CRISPR/Cas12, but other CRISPR/Cas families have been designed for nucleic acid detection.
Article
Chemistry, Multidisciplinary
Joon Soo Park, Kuangwen Hsieh, Liben Chen, Aniruddha Kaushik, Alexander Y. Trick, Tza-Huei Wang
Summary: The digital-enhanced CRISPR/Cas-assisted one-pot virus detection (deCOViD) is a novel assay that allows qualitative and quantitative detection of SARS-CoV-2 in a very short time with high sensitivity and a broad dynamic range. It outperforms current benchtop-based counterparts and represents one of the fastest and most sensitive CRISPR/Cas-assisted SARS-CoV-2 detection methods to date.
Review
Biochemical Research Methods
Mingzhu Yuan, Ronghua Ding, Shuaiyin Chen, Guangcai Duan
Summary: The CRISPR/Cas system provides a rapid and accurate nucleic acid detection method for on-site POCT, with features such as short detection cycles, low cost, and high sensitivity, which are crucial in interrupting outbreaks of infectious diseases.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biophysics
Xinkuan Cheng, Yaru Li, Jun Kou, Dan Liao, Wenlu Zhang, Lijuan Yin, Shuli Man, Long Ma
Summary: CRISPR/Cas tools have shown great potential in biosensing beyond gene editing. However, the application of CRISPR/Cas-based biosensors for non-nucleic acid targets is still in its early stages. This review summarizes the strategies and prospects of CRISPR/Cas toolboxes in recognizing non-nucleic acid targets, providing valuable information for the expansion of these powerful tools into multiple detection fields.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Biochemistry & Molecular Biology
Xiaoping Li, Jiaye Zhong, Haoyu Li, Yinbiao Qiao, Xiaolei Mao, Huayan Fan, Yiwu Zhong, Saber Imani, Shusen Zheng, Jianhui Li
Summary: CRISPR-Cas technology is a widely used gene editing tool in biology, microbiology, and other fields. It consists of highly conserved repetitive sequences and spacer sequences, and utilizes the endonuclease activity of Cas proteins, combined with signal amplification and transformation technologies, to rapidly detect pathogen nucleic acids.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biotechnology & Applied Microbiology
Lijuan Fang, Lusen Yang, Mingyue Han, Huimei Xu, Wenshuai Ding, Xuejun Dong
Summary: The CRISPR system, originally discovered in prokaryotes, is an immune mechanism that clears foreign nucleic acids. Its strong ability of gene editing, regulation and detection in eukaryotes has made it extensively applied in basic and applied research. This article reviews the biology, mechanisms and relevance of CRISPR-Cas technology, as well as its applications in the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The CRISPR technologies have been utilized in nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. The CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA molecules.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Chemistry, Analytical
Zhaohe Huang, Sitong Liu, Xiaojing Pei, Shujing Li, Yifan He, Yigang Tong, Guoqi Liu
Summary: This review discusses the importance and development of CRISPR/Cas system in nucleic acid detection applications. The combination of CRISPR with various signal-readout techniques has wide applications in molecular diagnostics. Fluorescence is a dominant read-out technique, and understanding fluorescence readout types and variables affecting the signals can improve experimental designs.
Article
Multidisciplinary Sciences
Sagar Sridhara, Hemant N. Goswami, Charlisa Whyms, Jonathan H. Dennis, Hong Li
Summary: CRISPR-Cas-based virus detection assays, particularly those utilizing Type III-A CRISPR-Cas system, offer rapid and sensitive detection of viruses like SARS-CoV-2, making them potentially valuable tools for disease diagnosis.
NATURE COMMUNICATIONS
(2021)
Review
Food Science & Technology
Jiali Qiao, Zhiying Zhao, Yaru Li, Minghui Lu, Shuli Man, Shengying Ye, Qiang Zhang, Long Ma
Summary: Food safety issues are of utmost importance in public health worldwide, and the development of rapid and effective detection methods is crucial. Nucleic acid isothermal amplification (NAIA) plays a significant role in food safety detection, and the integration of NAIA with the CRISPR/Cas system offers improved sensitivity, specificity, adaptability, versatility, and dependability. However, there is currently a lack of comprehensive summaries on the integration of NAIA and CRISPR/Cas in the field of food safety detection. This review comprehensively examines recent advances in CRISPR/Cas-integrated NAIA for food safety detection and discusses current challenges and future opportunities.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Review
Chemistry, Analytical
Annalisa Masi, Amina Antonacci, Maria Moccia, Valeria Frisulli, Mariarita De Felice, Mariarosaria De Falco, Viviana Scognamiglio
Summary: In addition to its remarkable genome editing capability, CRISPR-Cas system has proven to be effective in various applications, such as pathogenic infections, mutagenic defects, or early cancer diagnosis. However, further research is needed to address some drawbacks of CRISPR-Cas-based biosensors, such as target amplification, reproducibility, and robustness.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Siwenjie Qian, Yanju Chen, Xiaoli Xu, Cheng Peng, Xiaofu Wang, Hui Wu, Yang Liu, Xiaoping Zhong, Junfeng Xu, Jian Wu
Summary: This article reviews the recent advances of CRISPR-based amplification-free methods for nucleic acid detection, discusses the pros and cons of these methods, and further explores the challenges including sample preparation, off-target effect, sequences limit, quantitative and multiplex detection. It highlights the potential of CRISPR-powered detection methods to pave the way for rapid, cheap, highly sensitive and specific on-site detection without amplification.
ANALYTICAL BIOCHEMISTRY
(2022)
Article
Cell Biology
Lvyun Zhu, Li Nie, Sisi Xie, Ming Li, Chushu Zhu, Xinyuan Qiu, Jingyu Kuang, Chuanyang Liu, Chenyu Lu, Wenying Li, Er Meng, Dongyi Zhang, Lingyun Zhu
Summary: This study established a ground-based zebrafish disease model of microgravity to investigate the adverse effects of microgravity on the immune system, revealing that RIG-I-like receptor and Toll-like receptor signaling pathways are significantly compromised under simulated microgravity conditions. TRIM25, an essential factor for RLR signaling, is inhibited, disrupting the antiviral immune response feedback loop.
Article
Biotechnology & Applied Microbiology
Xiaomin Wu, Guang Ma, Chuanyang Liu, Xin-yuan Qiu, Lu Min, Jingyu Kuang, Lingyun Zhu
Summary: Pinene was successfully produced in R. sphaeroides through heterologous expression of GPPS-PS, and the production was greatly improved by optimizing key enzyme expression. This is the first report on pinene production by purple non-sulfur photosynthetic bacteria, expanding the potential for using photosynthetic chassis in pinene production.
MICROBIAL CELL FACTORIES
(2021)
Review
Cell Biology
Wenlun Wang, Lu Min, Xinyuan Qiu, Xiaomin Wu, Chuanyang Liu, Jiaxin Ma, Dongyi Zhang, Lingyun Zhu
Summary: Long non-coding RNAs (lncRNAs) play important roles in cellular functions by regulating target gene expression levels through epigenomic, transcriptional, and post-transcriptional approaches. Among them, long non-coding RNA X-inactive specific transcript (lncRNA Xist) acts as a crucial regulator in X chromosome inactivation and various disease processes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Immunology
Ruo-Ran Wang, Xinyuan Qiu, Ran Pan, Hongxing Fu, Ziyin Zhang, Qintao Wang, Haide Chen, Qing-Qian Wu, Xiaowen Pan, Yanping Zhou, Pengfei Shan, Shusen Wang, Guoji Guo, Min Zheng, Lingyun Zhu, Zhuo-Xian Meng
Summary: This study establishes a mouse model to investigate the adaptation process of pancreatic beta cells in response to high-fat diet (HFD) feeding. The findings show that dietary intervention can rescue beta cell dysfunction and reverse the changes in islet chromatin accessibility and transcriptome induced by HFD. The study also identifies CTCF as a key candidate gene involved in preserving beta cell function.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biology
Chuanyang Liu, Jingyu Kuang, Yuxuan Wang, Ting Duan, Lu Min, Chenyu Lu, Tianyi Zhang, Ruifen Chen, Ying Wu, Lingyun Zhu
Summary: This study provides a unique framework for researchers and clinicians to explore and understand the regulated biological functions of RNF8 in cancer. The identification of new targets and the close relationship between RNF8 and neurodegenerative diseases and tumor-infiltrating immune cells highlight the potential for developing targeted therapies against RNF8 in cancer.
Article
Biochemistry & Molecular Biology
Chuanyang Liu, Lu Min, Jingyu Kuang, Chushu Zhu, Xinyuan Qiu, Xiaomin Wu, Tianyi Zhang, Sisi Xie, Lingyun Zhu
Summary: This study investigates the specific roles of hsa-miR-654-5p in lung cancer and demonstrates its tumor-suppressing roles and prognostic values. The abundance of miR-654-5p is significantly elevated in LUAD tissues and correlates with patients' survival. In vitro experiments show that miR-654-5p inhibits the epithelial-mesenchymal transition (EMT) process, cell proliferation, and migration in lung cancer cells. The study also identifies potential target genes of miR-654-5p and develops a risk scoring model for assessing prognosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Chengan Lv, Yuchen Sun, Zhe Yu Zhang, Zeyad Aboelela, Xinyuan Qiu, Zhuo-Xian Meng
Summary: Pancreatic beta-cell dysfunction and insulin resistance are two main causes of type 2 diabetes (T2D), with dietary and exercise interventions being effective approaches for the treatment of obesity and T2D, particularly in the early stages. The functional capacity of beta-cells, especially in the first phase of insulin secretion, is crucial in the progression of T2D, and metabolic stresses play a key role in regulating beta-cell dynamics.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2022)
Article
Cell Biology
Junyi Song, Chuanyang Liu, Baoshan Li, Liangcheng Liu, Ling Zeng, Zonghuang Ye, Ting Mao, Wenjian Wu, Biru Hu
Summary: Reflectin proteins are natural copolymers that manipulate the structural coloration of cells. This study found differences in cellular localization among reflectin proteins, suggesting a possible evolutionary order. Additionally, reflectin proteins interact with the cytoskeleton, indicating its important role in their organization and transportation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Chenyu Lu, Jingyu Kuang, Tong Shao, Sisi Xie, Ming Li, Lingyun Zhu, Lvyun Zhu
Summary: Prime editing technology has shown attractive potential for versatile genome editing ability, but improvements are needed in terms of editing efficiency, off-target effects, and delivery systems. Recent optimizations have resulted in promising prospects for its application in various fields. This review provides a concise insight into the development, barriers, optimization efforts, and application directions of prime editing, offering clues for future advancements in this emerging field.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Jingya Xu, Xiaofei Li, Wei Chen, Ziyin Zhang, Yanping Zhou, Yahui Gou, Cheng-an Lv, Lu Jin, Xinyuan Qiu, Shengshan Ma, Qing-Qian Wu, Tongyu Liu, Lin Mi, Zhuoying Yang, Ting Yu, Xiaowen Pan, Yu Feng, Pengfei Shan, Zhuo-Xian Meng
Summary: Xu et al. have demonstrated that Baf60c plays a critical role in muscle regeneration by mediating paracrine signaling through Dkk3 in skeletal myofibers. They found that Baf60c interacts with Six4 to suppress Dkk3 expression in myocytes. This study also reveals the downregulation of Baf60c in obese and T2D individuals, and the upregulation of Dkk3 in muscle-specific Baf60c-deficient mice, leading to impaired muscle regeneration.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Cell Biology
Shuang Han, Qingqian Wu, Mengying Wang, Miqi Yang, Chen Sun, Jiaqi Liang, Xiaozhen Guo, Zheyu Zhang, Jingya Xu, Xinyuan Qiu, Cen Xie, Siyu Chen, Yue Gao, Zhuo-Xian Meng
Summary: Exercise intervention in obese mice can alleviate insulin resistance and glucose intolerance induced by a high-fat diet. Metabolomic and transcriptomic analyses revealed changes in metabolic pathways and gene expression profiles, indicating the beneficial effects of exercise intervention on systemic energy homeostasis.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tianyi Zhang, Chuanyang Liu, Wenying Li, Jingyu Kuang, Xin-yuan Qiu, Lu Min, Lingyun Zhu
Summary: This review summarizes the current state-of-the-art targeted protein degradation (TPD) technologies, including Trim-Away, LYTACs, and AUTACs, as well as their engineering efforts and developmental route. The general design principle, benefits, problems, and opportunities for improvement in TPD are analyzed, aiming to provide guidelines for the exploration, discovery, and future application of novel TPD tools.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
