1
|
Rao J, Wang X, Chen X, Liu Y, Jiang J, Wang Z. Multi-omics analysis reveals that Cas13d contributes to PI3K-AKT signaling and facilitates cell proliferation via PFKFB4 upregulation. Gene 2024; 927:148760. [PMID: 38992762 DOI: 10.1016/j.gene.2024.148760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
The CRISPR-Cas system is a powerful gene editing technology, the clinical application of which is currently constrained due to safety concerns. A substantial body of safety research concerning Cas9 exists; however, scant attention has been directed toward investigating the safety profile of the emergent Cas13 system, which confers RNA editing capabilities. In particular, uncertainties persist regarding the potential cellular impacts of Cas13d in the absence of reliance on a cleavage effect. In this study, we conducted an initial exploration of the effects of Cas13d on HeLa cells. Total RNA and protein samples were extracted after transfection with a Cas13d-expressing plasmid construct, followed by transcriptomic and proteomic sequencing. Differential gene expression analysis identified 94 upregulated and 847 downregulated genes, while differential protein expression analysis identified 185 upregulated and 231 downregulated proteins. Subsequently, enrichment analysis was conducted on the transcriptome and proteome sequencing data, revealing that the PI3K-Akt signaling pathway is a common term. After intersecting the differentially expressed genes enriched in the PI3K-Akt signaling pathway with all the differentially expressed proteins, it was found that the expression of the related regulatory gene PFKFB4 was upregulated. Moreover, western blot analysis demonstrated that Cas13d can mediate PI3K-Akt signaling upregulation through overexpression of PFKFB4. CCK-8 assay, colony formation, and EdU experiments showed that Cas13d can promote cell proliferation. Our data demonstrate, for the first time, that Cas13d significantly impacts the transcriptomic and proteomic profiles, and proliferation phenotype, of HeLa cells, thus offering novel insights into safety considerations regarding gene editing systems.
Collapse
Affiliation(s)
- Jin Rao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xuefu Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiangyu Chen
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yudi Liu
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Junfeng Jiang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China; Histology and Embryology Department, Naval Medical University, Shanghai, China.
| | - Zhinong Wang
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, China.
| |
Collapse
|
2
|
Wang T, Bai L, Wang G, Han J, Wu L, Chen X, Zhang H, Feng J, Wang Y, Wang R, Zhang X. SATCAS: A CRISPR/Cas13a-based simultaneous amplification and testing platform for one-pot RNA detection and SNPs distinguish in clinical diagnosis. Biosens Bioelectron 2024; 263:116636. [PMID: 39116631 DOI: 10.1016/j.bios.2024.116636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/18/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
The clinical diagnosis of pathogen infectious diseases increasingly requires sensitive and rapid RNA detection technologies. The RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a system has shown immense potential in molecular diagnostics due to its trans-cleavage activity. However, most Cas13a-based detection methods require an amplicon transcription step, and the multi-step open-tube operations are prone to contamination, limiting their widespread application. Here, we propose an ultrasensitive (single-copy range, ∼aM) and rapid (within 40 min) isothermal one-pot RNA detection platform, termed SATCAS (Simultaneous Amplification and Testing platform based on Cas13a). This method effectively distinguishes viable bacteria (0%-100%) under constant total bacterial conditions, demonstrating its robustness and universality. SATCAS excels in identifying single nucleotide polymorphisms (SNPs), particularly detecting 0.5% drug-resistant mutations. We validated SATCAS by detecting infections in biological samples from 68 HBV, 23 EBV, and 48 SARS-CoV-2 patients, achieving 100% sensitivity, 92.86% specificity, and 97.06% accuracy in HBV infection testing. We anticipate that SATCAS has broad application potential in the early diagnosis, subtyping, drug resistance detection, and point-of-care monitoring of pathogen infectious diseases.
Collapse
Affiliation(s)
- Ting Wang
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China
| | - Linlin Bai
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Guoling Wang
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China
| | - Jingli Han
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing, PR China; National Clinical Research Center for Hematologic Disease, Beijing, PR China
| | - Lixin Wu
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China
| | - Xuanzhong Chen
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China
| | - Hongyu Zhang
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China.
| | - Jia Feng
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, PR China.
| | - Yongming Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, PR China; Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 200438, PR China.
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, PR China; Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 200438, PR China; International Human Phenome Institutes, Shanghai, 200433, PR China.
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing, PR China; National Clinical Research Center for Hematologic Disease, Beijing, PR China.
| |
Collapse
|
3
|
Maleszka R. Reminiscences on the honeybee genome project and the rise of epigenetic concepts in insect science. INSECT MOLECULAR BIOLOGY 2024; 33:444-456. [PMID: 38196200 DOI: 10.1111/imb.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
The sequencing of the honeybee genome in 2006 was an important technological and logistic achievement experience. But what benefits have flown from the honeybee genome project? What does the annotated genomic assembly mean for the study of behavioural complexity and organismal function in honeybees? Here, I discuss several lines of research that have arisen from this project and highlight the rapidly expanding studies on insect epigenomics, emergent properties of royal jelly, the mechanism of nutritional control of development and the contribution of epigenomic regulation to the evolution of sociality. I also argue that the term 'insect epigenetics' needs to be carefully redefined to reflect the diversity of epigenomic toolkits in insects and the impact of lineage-specific innovations on organismal outcomes. The honeybee genome project helped pioneer advances in social insect molecular biology, and fuelled breakthrough research into the role of flexible epigenomic control systems in linking genotype to phenotype.
Collapse
Affiliation(s)
- Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| |
Collapse
|
4
|
Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
Collapse
Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| |
Collapse
|
5
|
Shang J, Song F, Zhang Z, Chen D, Yang S. Application of novel CRISPR tools in brain therapy. Life Sci 2024; 352:122855. [PMID: 38908787 DOI: 10.1016/j.lfs.2024.122855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
In recent years, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genome editing toolkit has been widely used to modify the genome sequence of organisms. As the CRISPR toolbox continues to grow and new CRISPR-associated (Cas) proteins are discovered, its applications have expanded beyond conventional genome editing. This now encompass epigenetic editing, gene expression control, and various other functions. Notably, these advancements are finding practical application in the treatment of brain diseases. Furthermore, the amalgamation of CRISPR and Chimeric Antigen Receptor T-cell (CAR-T) technologies has emerged as a potential approach for disease treatment. With this in mind, this review commences by offering a comprehensive overview of recent advancements in CRISPR gene editing tools. This encompasses an exploration of various Cas proteins, gene expression control, epigenetic editing, base editing and primer editing. Additionally, we present an in-depth examination of the manifold applications of these innovative CRISPR tools in the realms of brain therapeutics, such as neurodegenerative diseases, neurological syndromes and genetic disorders, epileptic disorders, and brain tumors, also explore the pathogenesis of these diseases. This includes their utilization in modeling, gene screening, therapeutic gene editing, as well as their emerging synergy with CAR-T technology. Finally, we discuss the remaining technical challenges that need to be addressed for effective utilization of CRISPR tools in disease treatment.
Collapse
Affiliation(s)
- Jiawen Shang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| | - Di Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| | - Sen Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| |
Collapse
|
6
|
You D, Xu T, Huang BZ, Wu F, Deng LS, Liu ZY, Ge LP, Liu ZH, Sun J, Zeng X, Zhou YC, Lai SY, Ai YR, Huang JB, Zhu L, Xu ZW. Rapid, sensitive, and visual detection of pseudorabies virus with an RPA-CRISPR/EsCas13d-based dual-readout portable platform. Anal Chim Acta 2024; 1318:342918. [PMID: 39067912 DOI: 10.1016/j.aca.2024.342918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Pseudorabies viruses (PRV) pose a major threat to the global pig industry and public health. Rapid, intuitive, affordable, and accurate diagnostic testing is critical for controlling and eradicating infectious diseases. In this study, a portable detection platform based on RPA-CRISPR/EsCas13d was developed. The platform exhibits high sensitivity (1 copy/μL), good specificity, and no cross-reactivity with common pathogens. The platform uses rapid preamplification technology to provide visualization results (lateral flow assays or visual fluorescence) within 1 h. Fifty pig samples (including tissues, oral fluids, and serum) were tested using this platform and real-time quantitative polymerase chain reaction (qPCR), showing 34.0 % (17 of 50) PRV positivity with the portable CRISPR/EsCas13d dual-readout platform, consistent with the qPCR results. These results highlight the stability, sensitivity, efficiency, and low equipment requirements of the portable platform. Additionally, a novel point-of-care test is being developed for clinical use in remote rural and resource-limited areas, which could be a prospective measure for monitoring the progression of pseudorabies and other infectious diseases worldwide.
Collapse
Affiliation(s)
- Dong You
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Tong Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bing-Zhou Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Fang Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li-Shuang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhe-Yan Liu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | | | | | - Jing Sun
- ChongQing Academy of Animal Sciences, China
| | - Xiu Zeng
- ChongQing Academy of Animal Sciences, China
| | - Yuan-Cheng Zhou
- Key Laboratory of Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China; Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Si-Yuan Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan-Ru Ai
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jian-Bo Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.
| | - Zhi-Wen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China; Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.
| |
Collapse
|
7
|
Upreti C, Kumar P, Durso LM, Palmer KL. CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure. Appl Environ Microbiol 2024:e0087624. [PMID: 39158272 DOI: 10.1128/aem.00876-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/24/2024] [Indexed: 08/20/2024] Open
Abstract
The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.
Collapse
Affiliation(s)
- Chahat Upreti
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Pranav Kumar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Lisa M Durso
- U.S. Department of Agriculture, Agricultural Research Service, Agroecosystem Management Unit, Lincoln, Nebraska, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| |
Collapse
|
8
|
Liu Y, Gou S, Qiu L, Xu Z, Yang H, Yang S, Zhao Y. A CRISPR/Cas12a-powered gold/nickel foam surface-enhanced Raman spectroscopy biosensor for nucleic acid specific detection in foods. Analyst 2024; 149:4343-4350. [PMID: 39051914 DOI: 10.1039/d4an00778f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Food is a necessary source of energy, but it also serves as a pathway for transmitting infectious pathogens, making food safety a matter of great concern. Rapid, accurate, and specific detection methods for foodborne viruses are crucial. Surface-Enhanced Raman Scattering (SERS), due to its superior sensitivity and characteristic fingerprint spectra, holds enormous potential. However, due to the limitations of SERS, it requires specific conditions to achieve specificity. In order to enhance the specificity and accuracy of nucleic acid detection based on SERS, we have developed a CRISPR-Cas12a-mediated SERS technique to identify target DNA, harnessing the targeting recognition capability of CRISPR-Cas12a and ultra-sensitive SERS tags and successfully addressing SERS' lack of specific detection capability. This system includes a gold/nickel foam substrate (Au-NFs) and a reporter (ssDNA-ROX). The phenomenon of colloidal gold/silver nano-aggregation due to magnesium ions, which is commonly encountered in CRISPR-SERS, was simultaneously solved using AuNFs. The qualitative and quantitative analysis of target DNA in drinking water was performed by monitoring the intensity change of ROX Raman reporter molecules. The results showed that the sensor detected DNA within 30 min and the limit of detection (LOD) was 8.23 fM. This is expected to become one of the alternative methods for nucleic acid detection for its rapid detection and high specificity.
Collapse
Affiliation(s)
- Yan Liu
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, China
| | - Shirui Gou
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Long Qiu
- Wuxi Tolo Biotechnology Co., Ltd, Wuxi, Jiangsu, China
| | - Zhiwen Xu
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Haifeng Yang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, China
| | - Shiping Yang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, China
| | - Yu Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| |
Collapse
|
9
|
Wang Y, Peng Y, Liu S, Li M, Pei X, Tong Y. CRISPR/Cas12a coupled with loop-mediated isothermal amplification and lateral flow assay for SARS-CoV-2 detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39158842 DOI: 10.1039/d4ay00757c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Point-of-care testing (POCT) is rapid, exhibits highly sensitive performance, can facilitate home self-testing and avoids cross-contamination. Herein, we developed a biosensor that combines Si-OH magnetic bead (MB)-based fast RNA extraction, reverse transcription-loop-mediated isothermal amplification (RT-LAMP), CRISPR-Cas12a, and lateral flow assay (LFA) for rapid detection of SARS-CoV-2 RNA within 1.5 h. In the presence of the SARS-CoV-2 LAMP amplicon, the trans-cleavage activity of Cas12a was activated to cleave the probe, separating streptavidin from the AuNPs-digoxin (Dig) antibody, resulting in the inability of the test line to capture the AuNPs-Dig antibody. The method can distinguish SARS-CoV-2 from other RNA viruses, with a limit-of-detection (LOD) of 6.2 × 102 copies per mL. Therefore, LAMP-CRISPR-LFA has high specificity and sensitivity and is convenient to develop into commercial assay kits, which could have a broad prospect for practical application.
Collapse
Affiliation(s)
- Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yadan Peng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Sitong Liu
- College of Chemistry and Materials Engineering, Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, P. R. China.
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Xiaojing Pei
- College of Chemistry and Materials Engineering, Institute of Cosmetic Regulatory Science, Beijing Technology and Business University, Beijing 100048, P. R. China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
10
|
Yoshimi K, Kuno A, Yamauchi Y, Hattori K, Taniguchi H, Mikamo K, Iida R, Ishida S, Goto M, Takeshita K, Ito R, Takahashi R, Takahashi S, Mashimo T. Genome editing using type I-E CRISPR-Cas3 in mice and rat zygotes. CELL REPORTS METHODS 2024; 4:100833. [PMID: 39121862 DOI: 10.1016/j.crmeth.2024.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
The type I CRISPR system has recently emerged as a promising tool, especially for large-scale genomic modification, but its application to generate model animals by editing zygotes had not been established. In this study, we demonstrate genome editing in zygotes using the type I-E CRISPR-Cas3 system, which efficiently generates deletions of several thousand base pairs at targeted loci in mice with 40%-70% editing efficiency without off-target mutations. To overcome the difficulties associated with detecting the variable deletions, we used a newly long-read sequencing-based multiplex genotyping approach. Demonstrating remarkable versatility, our Cas3-based technique was successfully extended to rats as well as mice, even by zygote electroporation methods. Knockin for SNP exchange and genomic replacement with a donor plasmid were also achieved in mice. This pioneering work with the type I CRISPR zygote editing system offers increased flexibility and broader applications in genetic engineering across different species.
Collapse
Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | - Akihiro Kuno
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kosuke Hattori
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiromi Taniguchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kouya Mikamo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ryuya Iida
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Saeko Ishida
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Motohito Goto
- Central Institute for Experimental Medicine and Life Science, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Kohei Takeshita
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Ryoji Ito
- Central Institute for Experimental Medicine and Life Science, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Riichi Takahashi
- Central Institute for Experimental Medicine and Life Science, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| |
Collapse
|
11
|
Gao Y, Zhang X, Wang X, Sun R, Li Y, Li J, Quan W, Yao Y, Hou Y, Li D, Sun Z. The clinical value of rapidly detecting urinary exosomal lncRNA RMRP in bladder cancer with an RT-RAA-CRISPR/Cas12a method. Clin Chim Acta 2024; 562:119855. [PMID: 38981565 DOI: 10.1016/j.cca.2024.119855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/25/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND AND AIMS Bladder cancer (BCa) is a highly aggressive malignancy of the urinary system. Timely detection is imperative for enhancing BCa patient prognosis. MATERIALS AND METHODS This study introduces a novel approach for detecting long non-coding RNA (lncRNA) Mitochondrial RNA Processing Endoribonuclease (RMRP) in urine exosomes from BCa patients using the reverse transcription recombinase-aided amplification (RT-RAA) and clustered regularly interspaced short palindromic repeats and associated Cas12a proteins (CRISPR/Cas12a) technique. Various statistical methods were used to evaluate its diagnostic value for BCa. RESULTS The specificity of urine exosomal RMRP detection for BCa diagnosis was enhanced by using RT-RAA combined with CRISPR/Cas12a. The testing process duration was reduced to 30 min, which supports rapid detection. Moreover, this approach allows the identification of target signals in real-time using blue light, facilitating immediate detection. In clinical sample analysis, this methodology exhibited a high level of diagnostic efficacy. This was evidenced by larger area under the curve values with receiver operating characteristic curve analysis compared with using traditional RT-qPCR methods, indicating superior diagnostic accuracy and sensitivity. Furthermore, the combined analysis of RMRP expression in urine exosomes detected by RT-RAA-CRISPR/Cas12a and NMP-22 expression may further enhance diagnostic accuracy. CONCLUSIONS The RT-RAA-CRISPR/Cas12a technology is a swift, sensitive, and uncomplicated method for nucleic acid detection. Because of its convenient and non-invasive sampling approach, user-friendly operation, and reproducibility, this technology is very promising for automated detection and holds favorable application possibilities within clinical environments.
Collapse
Affiliation(s)
- Yuting Gao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Xueru Zhang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Xuanlin Wang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Ruixin Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yaran Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Jing Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Wenqiang Quan
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yiwen Yao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yanqiang Hou
- Department of Clinical Laboratory, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, PR China.
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China.
| | - Zujun Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China.
| |
Collapse
|
12
|
Shen X, Lin Z, Jiang X, Zhu X, Zeng S, Cai S, Liu H. Dumbbell probe initiated multi-rolling circle amplification assisted CRISPR/Cas12a for highly sensitive detection of clinical microRNA. Biosens Bioelectron 2024; 264:116676. [PMID: 39151261 DOI: 10.1016/j.bios.2024.116676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
A novel miRNA detection technique named Dumbbell probe initiated multi-Rolling Circle Amplification assisted CRISPR/Cas12a (DBmRCA) was developed relying on the ligation-free dumbbell probe and the high-sensitivity CRISPR/Cas12a signal out strategy. This DBmRCA assay streamlines miRNA quantification within a mere 30-min timeframe and with exceptional analytical precision. The efficacy of this method was validated by assessing miRNA levels in clinical samples, revealing distinct expression panel of miR-200a and miR-126 in lung cancer/adjacent/normal tissue specimens. Moreover, a predictive model was established to classify benign and malignant tumor. Due to its time efficiency, enhanced sensitivity, and streamlined workflow, this assay would be a reliable tool for miRNA analysis in clinical settings, offering potential guidance for early diagnosis and treatment of lung cancer.
Collapse
Affiliation(s)
- Xudan Shen
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Ziwei Lin
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Xianfeng Jiang
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Xinlan Zhu
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Su Zeng
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Sheng Cai
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China; Jinhua Institute of Zhejiang University, Jinhua, 321299, Zhejiang, China.
| | - Hui Liu
- Clinical Research Center, Sir Run Run Shaw Hospital, School of Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310020, Zhejiang, China.
| |
Collapse
|
13
|
Ohtani H, Liu M, Liang G, Jang HJ, Jones PA. Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms. Nucleic Acids Res 2024; 52:8205-8217. [PMID: 38874474 DOI: 10.1093/nar/gkae498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Long terminal repeats (LTRs), which often contain promoter and enhancer sequences of intact endogenous retroviruses (ERVs), are known to be co-opted as cis-regulatory elements for fine-tuning host-coding gene expression. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, substantial activation of LTRs has been found in human cells after treatment with epigenetic inhibitors. Although the LTR12C family makes up the majority of ERVs activated by epigenetic inhibitors, how these epigenetically and transcriptionally activated LTR12C elements can regulate the host-coding gene expression remains unclear due to genome-wide alteration of transcriptional changes after epigenetic inhibitor treatments. Here, we specifically transactivated >600 LTR12C elements by using single guide RNA-based dCas9-SunTag-VP64, a site-specific targeting CRISPR activation (CRISPRa) system, with minimal off-target events. Interestingly, most of the transactivated LTR12C elements acquired the H3K27ac-marked enhancer feature, while only 20% were co-marked with promoter-associated H3K4me3 modifications. The enrichment of the H3K4me3 signal was intricately associated with downstream regions of LTR12C, such as internal regions of intact ERV9 or other types of retrotransposons. Here, we leverage an optimized CRISPRa system to identify two distinct epigenetic signatures that define LTR12C transcriptional activation, which modulate the expression of proximal protein-coding genes.
Collapse
Affiliation(s)
- Hitoshi Ohtani
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Minmin Liu
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - H Josh Jang
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Peter A Jones
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| |
Collapse
|
14
|
Wang Q, Ma C, Mao H, Wang J. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates the ZNF334 gene to inhibit the growth of colorectal cancer. Int J Biol Macromol 2024; 277:134580. [PMID: 39122070 DOI: 10.1016/j.ijbiomac.2024.134580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Although therapeutic targets for colorectal cancer (CRC) treatment have been developed, the treatment outcomes are not ideal and survival rates for CRC patients remain low. It is critical to identify a specific target and develop an effective CRC treatment system. The ZNF334 gene is a newly identified member of Zinc-finger proteins (ZNFs), which is essential for key biological processes associated with tumorigenesis. Abnormal epigenetic reprogramming of the ZNF334 gene promoter region decreases its expression in CRC and further induces the occurrence of CRC. Here, we clarified that P300 in CRC can regulate the H3K9/27 ac in the ZNF334 promoter. Furthermore, histone acetylation of the ZNF334 promoter region was increased by dCas9-P300 to normalize the deficiency of ZNF334 expression, thereby inhibiting the growth of CRC. Collectively, our findings enable a facile way to affect gene expression using CRISPR/Cas9-based epigenome editing and further determine the causal link between histone acetylation and gene activation, providing a promising gene therapy strategy for the CRC treatment.
Collapse
Affiliation(s)
- Qin Wang
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China; BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Chen Ma
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Huixian Mao
- School of Pharmacy, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jin Wang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China.
| |
Collapse
|
15
|
Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
Collapse
Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
| |
Collapse
|
16
|
Le Franc A, Da Silva A, Lepetre-Mouelhi S. Nanomedicine and voltage-gated sodium channel blockers in pain management: a game changer or a lost cause? Drug Deliv Transl Res 2024; 14:2112-2145. [PMID: 38861139 DOI: 10.1007/s13346-024-01615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Pain, a complex and debilitating condition affecting millions globally, is a significant concern, especially in the context of post-operative recovery. This comprehensive review explores the complexity of pain and its global impact, emphasizing the modulation of voltage-gated sodium channels (VGSC or NaV channels) as a promising avenue for pain management with the aim of reducing reliance on opioids. The article delves into the role of specific NaV isoforms, particularly NaV 1.7, NaV 1.8, and NaV 1.9, in pain process and discusses the development of sodium channel blockers to target these isoforms precisely. Traditional local anesthetics and selective NaV isoform inhibitors, despite showing varying efficacy in pain management, face challenges in systemic distribution and potential side effects. The review highlights the potential of nanomedicine in improving the delivery of local anesthetics, toxins and selective NaV isoform inhibitors for a targeted and sustained release at the site of pain. This innovative strategy seeks to improve drug bioavailability, minimize systemic exposure, and optimize therapeutic outcomes, holding significant promise for secure pain management and enhancing the quality of life for individuals recovering from surgical procedures or suffering from chronic pain.
Collapse
Affiliation(s)
- Adélaïde Le Franc
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Alexandre Da Silva
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | | |
Collapse
|
17
|
Feng Q, Li Q, Zhou H, Wang Z, Lin C, Jiang Z, Liu T, Wang D. CRISPR technology in human diseases. MedComm (Beijing) 2024; 5:e672. [PMID: 39081515 PMCID: PMC11286548 DOI: 10.1002/mco2.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Gene editing is a growing gene engineering technique that allows accurate editing of a broad spectrum of gene-regulated diseases to achieve curative treatment and also has the potential to be used as an adjunct to the conventional treatment of diseases. Gene editing technology, mainly based on clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein systems, which is capable of generating genetic modifications in somatic cells, provides a promising new strategy for gene therapy for a wide range of human diseases. Currently, gene editing technology shows great application prospects in a variety of human diseases, not only in therapeutic potential but also in the construction of animal models of human diseases. This paper describes the application of gene editing technology in hematological diseases, solid tumors, immune disorders, ophthalmological diseases, and metabolic diseases; focuses on the therapeutic strategies of gene editing technology in sickle cell disease; provides an overview of the role of gene editing technology in the construction of animal models of human diseases; and discusses the limitations of gene editing technology in the treatment of diseases, which is intended to provide an important reference for the applications of gene editing technology in the human disease.
Collapse
Affiliation(s)
- Qiang Feng
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Qirong Li
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Hengzong Zhou
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Zhan Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Chao Lin
- School of Grain Science and TechnologyJilin Business and Technology CollegeChangchunChina
| | - Ziping Jiang
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
| | - Tianjia Liu
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Dongxu Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
| |
Collapse
|
18
|
Miao P, Sun Y, Zheng G, Wang B, Wang W, Zhang J, Yan M, Lv Y. Near-infrared light-induced homogeneous photoelectrochemical biosensor based on 3D walking nanomotor-assisted CRISPR/Cas12a for ultrasensitive microRNA-155 detection. J Colloid Interface Sci 2024; 667:82-90. [PMID: 38621334 DOI: 10.1016/j.jcis.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
The dysregulation of microRNA (miRNA) expression levels is intricately linked to a myriad of human diseases, and the precise and delicate detection thereof holds paramount significance in the realm of clinical diagnosis and therapy. Herein, a near-infrared (NIR) light-mediated homogeneous photoelectrochemical (PEC) biosensor was constructed for miRNA-155 detection based on NaYF4: Yb, Tm@ZnIn2S4 (NYF@ ZIS) coupled with a three-dimensional (3D) walking nanomotor-assisted CRISPR/Cas12a strategy. The upconverted light emitted by the NYF in the visible and UV region upon NIR light excitation could be utilized to excite ZIS to produce a photocurrent response. The presence of target miRNA-155 initiated an amplification reaction within the 3D walking nanomotor, resulting in the production of multiple nucleic acid fragments. These fragments could activate the collateral cleavage capability of CRISPR/Cas12a, leading to the indiscriminate cleavage of single-stranded DNA (ssDNA) on ALP-ssDNA-modified magnetic beads and the subsequent liberation of alkaline phosphatase (ALP). The released ALP facilitated the catalysis of ascorbic acid 2-phosphate to generate ascorbic acid as the electron donor to capture the photogenerated holes on the NYF@ZIS surface, resulting in a positively correlated alteration in the photocurrent response. Under optimal conditions, the NIR light-initiated homogeneous PEC biosensor had the merits of good linear range (0.1 fM to 100 pM), an acceptable limit of detection (65.77 aM) for miRNA-155 detection. Considering the pronounced sensitivity, light stability, and low photodamage, this strategy presents a promising platform for detecting various other miRNA biomarkers in molecular diagnostic practice.
Collapse
Affiliation(s)
- Pei Miao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Yan Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Gengxiu Zheng
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Bin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Wenshou Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China
| | - Jing Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China.
| | - Mei Yan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, PR China.
| | - Yanfeng Lv
- Department of Colorectal & Anal Surgery, The Second Hospital of Shandong University, Jinan 250033, PR China.
| |
Collapse
|
19
|
Wang H, Hang X, Wang H, Peng J, Yu H, Wang L. Label/immobilization-free Cas12a-based electrochemiluminescence biosensor for sensitive DNA detection. Talanta 2024; 275:126114. [PMID: 38631265 DOI: 10.1016/j.talanta.2024.126114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Electrochemiluminescence (ECL) is one of the most sensitive techniques in the field of diagnostics. However, they typically require luminescent labeling and electrode surface biological modification, which is a time-consuming and laborious process involving multiple steps and may also lead to low reaction efficiency. Fabricating label/modification-free biosensors has become one of the most attractive parts for simplifying the ECL assays. In this work, the ECL luminophores carbon dots (CDs) were encapsulated in DNA hydrogel in situ by a simple rolling circle amplification (RCA) reaction. Upon binding of the target DNA, active Cas12a induces a collateral cleavage of the hydrogel's ssDNA backbone, resulting in a programmable degradation of the hydrogel and the release of CDs. By directly measuring the released CDs ECL, a simple and rapid label/modification-free detection of the target HPV-16 was realized. It is noted that this method allowed for 0.63 pM HPV-16 DNA detection without any amplification step, and it could take only ∼60 min for a fast test of a human serum sample. These results showed that our label/modification-free ECL biosensor has great potential for use in simple, rapid, and sensitive point-of-care (POC) detection.
Collapse
Affiliation(s)
- Honghong Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Xiaomin Hang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Huiyi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jiaxin Peng
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Haoming Yu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Li Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China.
| |
Collapse
|
20
|
De Castro V, Galaine J, Loyon R, Godet Y. CRISPR-Cas gene knockouts to optimize engineered T cells for cancer immunotherapy. Cancer Gene Ther 2024; 31:1124-1134. [PMID: 38609574 DOI: 10.1038/s41417-024-00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
While CAR-T and tgTCR-T therapies have exhibited noteworthy and promising outcomes in hematologic and solid tumors respectively, a set of distinct challenges remains. Consequently, the quest for novel strategies has become imperative to safeguard and more effectively release the full functions of engineered T cells. These factors are intricately linked to the success of adoptive cell therapy. Recently, CRISPR-based technologies have emerged as a major breakthrough for maintaining T cell functions. These technologies have allowed the discovery of T cells' negative regulators such as specific cell-surface receptors, cell-signaling proteins, and transcription factors that are involved in the development or maintenance of T cell dysfunction. By employing a CRISPR-genic invalidation approach to target these negative regulators, it has become possible to prevent the emergence of hypofunctional T cells. This review revisits the establishment of the dysfunctional profile of T cells before delving into a comprehensive summary of recent CRISPR-gene invalidations, with each invalidation contributing to the enhancement of engineered T cells' antitumor capacities. The narrative unfolds as we explore how these advancements were discovered and identified, marking a significant advancement in the pursuit of superior adoptive cell therapy.
Collapse
Affiliation(s)
- Valentine De Castro
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Jeanne Galaine
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Romain Loyon
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France
| | - Yann Godet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000, Besançon, France.
| |
Collapse
|
21
|
Choudry MW, Riaz R, Nawaz P, Ashraf M, Ijaz B, Bakhsh A. CRISPR-Cas9 mediated understanding of plants' abiotic stress-responsive genes to combat changing climatic patterns. Funct Integr Genomics 2024; 24:132. [PMID: 39078500 DOI: 10.1007/s10142-024-01405-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/31/2024]
Abstract
Multiple abiotic stresses like extreme temperatures, water shortage, flooding, salinity, and exposure to heavy metals are confronted by crop plants with changing climatic patterns. Prolonged exposure to these adverse environmental conditions leads to stunted plant growth and development with significant yield loss in crops. CRISPR-Cas9 genome editing tool is being frequently employed to understand abiotic stress-responsive genes. Noteworthy improvements in CRISPR-Cas technology have been made over the years, including upgradation of Cas proteins fidelity and efficiency, optimization of transformation protocols for different crop species, base and prime editing, multiplex gene-targeting, transgene-free editing, and graft-based heritable CRISPR-Cas9 approaches. These developments helped to improve the knowledge of abiotic stress tolerance in crops that could potentially be utilized to develop knock-out varieties and over-expressed lines to tackle the adverse effects of altered climatic patterns. This review summarizes the mechanistic understanding of heat, drought, salinity, and metal stress-responsive genes characterized so far using CRISPR-Cas9 and provides data on potential candidate genes that can be exploited by modern-day biotechnological tools to develop transgene-free genome-edited crops with better climate adaptability. Furthermore, the importance of early-maturing crop varieties to withstand abiotic stresses is also discussed in this review.
Collapse
Affiliation(s)
| | - Rabia Riaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Pashma Nawaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Maria Ashraf
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| |
Collapse
|
22
|
Bayat M, Nahand JS. Let's make it personal: CRISPR tools in manipulating cell death pathways for cancer treatment. Cell Biol Toxicol 2024; 40:61. [PMID: 39075259 PMCID: PMC11286699 DOI: 10.1007/s10565-024-09907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
Advancements in the CRISPR technology, a game-changer in experimental research, have revolutionized various fields of life sciences and more profoundly, cancer research. Cell death pathways are among the most deregulated in cancer cells and are considered as critical aspects in cancer development. Through decades, our knowledge of the mechanisms orchestrating programmed cellular death has increased substantially, attributed to the revolution of cutting-edge technologies. The heroic appearance of CRISPR systems have expanded the available screening platform and genome engineering toolbox to detect mutations and create precise genome edits. In that context, the precise ability of this system for identification and targeting of mutations in cell death signaling pathways that result in cancer development and therapy resistance is an auspicious choice to transform and accelerate the individualized cancer therapy. The concept of personalized cancer therapy stands on the identification of molecular characterization of the individual tumor and its microenvironment in order to provide a precise treatment with the highest possible outcome and minimum toxicity. This study explored the potential of CRISPR technology in precision cancer treatment by identifying and targeting specific cell death pathways. It showed the promise of CRISPR in finding key components and mutations involved in programmed cell death, making it a potential tool for targeted cancer therapy. However, this study also highlighted the challenges and limitations that need to be addressed in future research to fully realize the potential of CRISPR in cancer treatment.
Collapse
Affiliation(s)
- Mobina Bayat
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran.
| |
Collapse
|
23
|
Yang P, Lou Y, Geng Z, Guo Z, Wu S, Li Y, Song K, Shi T, Zhang S, Xiong J, Chen AF, Li D, Pu WT, Da L, Zhang Y, Sun K, Zhang B. Allele-Specific Suppression of Variant MHC With High-Precision RNA Nuclease CRISPR-Cas13d Prevents Hypertrophic Cardiomyopathy. Circulation 2024; 150:283-298. [PMID: 38752340 PMCID: PMC11259241 DOI: 10.1161/circulationaha.123.067890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/12/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Familial hypertrophic cardiomyopathy has severe clinical complications of heart failure, arrhythmia, and sudden cardiac death. Heterozygous single nucleotide variants (SNVs) of sarcomere genes such as MYH7 are the leading cause of this type of disease. CRISPR-Cas13 (clustered regularly interspaced short palindromic repeats and their associated protein 13) is an emerging gene therapy approach for treating genetic disorders, but its therapeutic potential in genetic cardiomyopathy remains unexplored. METHODS We developed a sensitive allelic point mutation reporter system to screen the mutagenic variants of Cas13d. On the basis of Cas13d homology structure, we rationally designed a series of Cas13d variants and obtained a high-precision Cas13d variant (hpCas13d) that specifically cleaves the MYH7 variant RNAs containing 1 allelic SNV. We validated the high precision and low collateral cleavage activity of hpCas13d through various in vitro assays. We generated 2 HCM mouse models bearing distinct MYH7 SNVs and used adenovirus-associated virus serotype 9 to deliver hpCas13d specifically to the cardiomyocytes. We performed a large-scale library screening to assess the potency of hpCas13d in resolving 45 human MYH7 allelic pathogenic SNVs. RESULTS Wild-type Cas13d cannot distinguish and specifically cleave the heterozygous MYH7 allele with SNV. hpCas13d, with 3 amino acid substitutions, had minimized collateral RNase activity and was able to resolve various human MYH7 pathological sequence variations that cause hypertrophic cardiomyopathy. In vivo application of hpCas13d to 2 hypertrophic cardiomyopathy models caused by distinct human MYH7 analogous sequence variations specifically suppressed the altered allele and prevented cardiac hypertrophy. CONCLUSIONS Our study unveils the great potential of CRISPR-Cas nucleases with high precision in treating inheritable cardiomyopathy and opens a new avenue for therapeutic management of inherited cardiac diseases.
Collapse
Affiliation(s)
- Ping Yang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Yingmei Lou
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Zhizhao Guo
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Shuo Wu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Yige Li
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Kaiyuan Song
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China (T.S.)
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Junhao Xiong
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Alex F. Chen
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China (D.L.)
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, MA (W.T.P.)
- Harvard Stem Cell Institute, Harvard University, MA (W.T.P.)
| | - Lintai Da
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Yan Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China (Y.Z.)
| | - Kun Sun
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Engineering Research Center of Techniques and Instruments for Diagnosis and Treatment of Congenital Heart Disease, Institute for Developmental and Regenerative Medicine, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China (P.Y., Y. Lou, Z. Geng, Z. Guo, S.W., Y. Li, K.S., S.Z., J.X., A.F.C., L.D., K.S., B.Z.)
| |
Collapse
|
24
|
Cao Y, Li X, Pan Y, Wang H, Yang S, Hong L, Ye L. CRISPR-based genetic screens advance cancer immunology. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2571-0. [PMID: 39048715 DOI: 10.1007/s11427-023-2571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/18/2024] [Indexed: 07/27/2024]
Abstract
CRISPR technologies have revolutionized research areas ranging from fundamental science to translational medicine. CRISPR-based genetic screens offer a powerful platform for unbiased screening in various fields, such as cancer immunology. Immune checkpoint blockade (ICB) therapy has been shown to strongly affect cancer treatment. However, the currently available ICBs are limited and do not work in all cancer patients. Pooled CRISPR screens enable the identification of previously unknown immune regulators that can regulate T-cell activation, cytotoxicity, persistence, infiltration into tumors, cytokine secretion, memory formation, T-cell metabolism, and CD4+ T-cell differentiation. These novel targets can be developed as new immunotherapies or used with the current ICBs as new combination therapies that may yield synergistic efficacy. Here, we review the progress made in the development of CRISPR technologies, particularly technological advances in CRISPR screens and their application in novel target identification for immunotherapy.
Collapse
Affiliation(s)
- Yuanfang Cao
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Xueting Li
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Yumu Pan
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Huahe Wang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Siyu Yang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lingjuan Hong
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lupeng Ye
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China.
| |
Collapse
|
25
|
Carrier L. RNA Editing Holds Promise for Hypertrophic Cardiomyopathy Therapy. Circulation 2024; 150:299-301. [PMID: 39038091 DOI: 10.1161/circulationaha.124.070137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Affiliation(s)
- Lucie Carrier
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
26
|
Chen F, Zhang C, Xue J, Wang F, Li Z. Molecular mechanism for target RNA recognition and cleavage of Cas13h. Nucleic Acids Res 2024; 52:7279-7291. [PMID: 38661236 PMCID: PMC11229369 DOI: 10.1093/nar/gkae324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
RNA-targeting type VI CRISPR-Cas effectors are widely used in RNA applications. Cas13h is a recently identified subtype of Cas13 ribonuclease, with strong RNA cleavage activity and robust in vivo RNA knockdown efficiency. However, little is known regarding its biochemical properties and working mechanisms. Biochemical characterization of Cas13h1 indicated that it lacks in vitro pre-crRNA processing activity and adopts a central seed. The cleavage activity of Cas13h1 is enhanced by a R(G/A) 5'-PFS, and inhibited by tag:anti-tag RNA pairing. We determined the structures of Cas13h1-crRNA binary complex at 3.1 Å and Cas13h1-crRNA-target RNA ternary complex at 3.0 Å. The ternary complex adopts an elongated architecture, and encodes a nucleotide-binding pocket within Helical-2 domain to recognize the guanosine at the 5'-end of the target RNA. Base pairing between crRNA guide and target RNA disrupts Cas13h1-guide interactions, leading to dramatic movement of HEPN domains. Upon target RNA engagement, Cas13h1 adopts a complicated activation mechanism, including separation of HEPN catalytic residues and destabilization of the active site loop and NTD domain, to get activated. Collectively, these insights expand our understanding into Cas13 effectors.
Collapse
Affiliation(s)
- Fugen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jialin Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| |
Collapse
|
27
|
Yan H, Tang W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat Chem Biol 2024:10.1038/s41589-024-01661-x. [PMID: 38969862 DOI: 10.1038/s41589-024-01661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
Programmed RNA editing presents an attractive therapeutic strategy for genetic disease. In this study, we developed bacterial deaminase-enabled recoding of RNA (DECOR), which employs an evolved Escherichia coli transfer RNA adenosine deaminase, TadA8e, to deposit adenosine-to-inosine editing to CRISPR-specified sites in the human transcriptome. DECOR functions in a variety of cell types, including human lung fibroblasts, and delivers on-target activity similar to ADAR-overexpressing RNA-editing platforms with 88% lower off-target effects. High-fidelity DECOR further reduces off-target effects to basal level. We demonstrate the clinical potential of DECOR by targeting Van der Woude syndrome-causing interferon regulatory factor 6 (IRF6) insufficiency. DECOR-mediated RNA editing removes a pathogenic upstream open reading frame (uORF) from the 5' untranslated region of IRF6 and rescues primary ORF expression from 12.3% to 36.5%, relative to healthy transcripts. DECOR expands the current portfolio of effector proteins and opens new territory in programmed RNA editing.
Collapse
Affiliation(s)
- Hao Yan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
28
|
Rooholamini Z, Dianat-Moghadam H, Esmaeilifallah M, Khanahmad H. From classical approaches to new developments in genetic engineering of live attenuated vaccine against cutaneous leishmaniasis: potential and immunization. Front Public Health 2024; 12:1382996. [PMID: 39035184 PMCID: PMC11257927 DOI: 10.3389/fpubh.2024.1382996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/07/2024] [Indexed: 07/23/2024] Open
Abstract
Despite the development of a vaccine against cutaneous leishmaniasis in preclinical and clinical studies, we still do not have a safe and effective vaccine for human use. Given this situation, the search for a new prophylactic alternative to control leishmaniasis should be a global priority. A first-generation vaccine strategy-leishmanization, in which live Leishmania major parasites are inoculated into the skin to protect against reinfection, is taking advantage of this situation. Live attenuated Leishmania vaccine candidates are promising alternatives due to their robust protective immune responses. Importantly, they do not cause disease and could provide long-term protection following challenges with a virulent strain. In addition to physical and chemical methods, genetic tools, including the Cre-loxP system, have enabled the selection of safer null mutant live attenuated Leishmania parasites obtained by gene disruption. This was followed by the discovery and introduction of CRISPR/Cas-based gene editing tools, which can be easily and precisely used to modify genes. Here, we briefly review the immunopathology of L. major parasites and then present the classical methods and their limitations for the production of live attenuated vaccines. We then discuss the potential of current genetic engineering tools to generate live attenuated vaccine strains by targeting key genes involved in L. major pathogenesis and then discuss their discovery and implications for immune responses to control leishmaniasis.
Collapse
Affiliation(s)
- Zahra Rooholamini
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Dianat-Moghadam
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahsa Esmaeilifallah
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
29
|
Smith DJ, Lunj S, Adamson AD, Nagarajan S, Smith TAD, Reeves KJ, Hoskin PJ, Choudhury A. CRISPR-Cas9 potential for identifying novel therapeutic targets in muscle-invasive bladder cancer. Nat Rev Urol 2024:10.1038/s41585-024-00901-y. [PMID: 38951705 DOI: 10.1038/s41585-024-00901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 07/03/2024]
Abstract
Gene editing technologies help identify the genetic perturbations driving tumour initiation, growth, metastasis and resistance to therapeutics. This wealth of information highlights tumour complexity and is driving cancer research towards precision medicine approaches based on an individual's tumour genetics. Bladder cancer is the 11th most common cancer in the UK, with high rates of relapse and low survival rates in patients with muscle-invasive bladder cancer (MIBC). MIBC is highly heterogeneous and encompasses multiple molecular subtypes, each with different responses to therapeutics. This evidence highlights the need to identify innovative therapeutic targets to address the challenges posed by this heterogeneity. CRISPR-Cas9 technologies have been used to advance our understanding of MIBC and determine novel drug targets through the identification of drug resistance mechanisms, targetable cell-cycle regulators, and novel tumour suppressor and oncogenes. However, the use of these technologies in the clinic remains a substantial challenge and will require careful consideration of dosage, safety and ethics. CRISPR-Cas9 offers considerable potential for revolutionizing bladder cancer therapies, but substantial research is required for validation before these technologies can be used in the clinical setting.
Collapse
Affiliation(s)
- Danielle J Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK.
| | - Sapna Lunj
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health Research and Innovation, University of Manchester, Manchester, UK
| | - Sankari Nagarajan
- Division of Molecular and Cellular Function, University of Manchester, Manchester, UK
| | - Tim A D Smith
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Nuclear Futures Institute, Bangor University, Bangor, UK
| | | | - Peter J Hoskin
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| |
Collapse
|
30
|
Zhou L, Simonian AL. CRISPR/Cas Technology: The Unique Synthetic Biology Genome-Editing Tool Shifting the Paradigm in Viral Diagnostics, Defense, and Therapeutics. Annu Rev Biomed Eng 2024; 26:247-272. [PMID: 38346278 DOI: 10.1146/annurev-bioeng-081723-013033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The emergence of the COVID-19 pandemic has starkly exposed our significantly limited ability to promptly identify and respond to emergent biological threats. Consequently, there is an urgent need to advance biotechnological methods for addressing both known and unforeseen biological hazards. Recently, the CRISPR/Cas system has revolutionized genetic engineering, enabling precise and efficient synthetic biology applications. Therefore, this review aims to provide a comprehensive introduction to the fundamental principles underlying the CRISPR/Cas system and assess the advantages and limitations of various CRISPR/Cas-based techniques applicable to the detection of, defense against, and treatment of viral infections. These techniques include viral diagnostics, the development of antiviral vaccines, B cell engineering for antibody production, viral activation/interference, and epigenetic modifications. Furthermore, this review delves into the challenges and bioethical considerations associated with use of the CRISPR/Cas system. With the continuous evolution of technology, the CRISPR/Cas system holds considerable promise for addressing both existing and unforeseen biological threats.
Collapse
Affiliation(s)
- Lang Zhou
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
| | - Aleksandr L Simonian
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
| |
Collapse
|
31
|
Hosseini SY, Mallick R, Mäkinen P, Ylä-Herttuala S. Insights into Prime Editing Technology: A Deep Dive into Fundamentals, Potentials, and Challenges. Hum Gene Ther 2024. [PMID: 38832869 DOI: 10.1089/hum.2024.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
As the most versatile and precise gene editing technology, prime editing (PE) can establish a durable cure for most human genetic disorders. Several generations of PE have been developed based on an editor machine or prime editing guide RNA (pegRNA) to achieve any kind of genetic correction. However, due to the early stage of development, PE complex elements need to be optimized for more efficient editing. Smart optimization of editor proteins as well as pegRNA has been contemplated by many researchers, but the universal PE machine's current shortcomings remain to be solved. The modification of PE elements, fine-tuning of the host genes, manipulation of epigenetics, and blockage of immune responses could be used to reach more efficient PE. Moreover, the host factors involved in the PE process, such as repair and innate immune system genes, have not been determined, and PE cell context dependency is still poorly understood. Regarding the large size of the PE elements, delivery is a significant challenge and the development of a universal viral or nonviral platform is still far from complete. PE versions with shortened variants of reverse transcriptase are still too large to fit in common viral vectors. Overall, PE faces challenges in optimization for efficiency, high context dependency during the cell cycling, and delivery due to the large size of elements. In addition, immune responses, unpredictability of outcomes, and off-target effects further limit its application, making it essential to address these issues for broader use in nonpersonalized gene editing. Besides, due to the limited number of suitable animal models and computational modeling, the prediction of the PE process remains challenging. In this review, the fundamentals of PE, including generations, potential, optimization, delivery, in vivo barriers, and the future landscape of the technology are discussed.
Collapse
Affiliation(s)
- Seyed Younes Hosseini
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petri Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| |
Collapse
|
32
|
Kansal R. The CRISPR-Cas System and Clinical Applications of CRISPR-Based Gene Editing in Hematology with a Focus on Inherited Germline Predisposition to Hematologic Malignancies. Genes (Basel) 2024; 15:863. [PMID: 39062641 PMCID: PMC11276294 DOI: 10.3390/genes15070863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has begun to transform the treatment landscape of genetic diseases. The history of the discovery of CRISPR/CRISPR-associated (Cas) proteins/single-guide RNA (sgRNA)-based gene editing since the first report of repetitive sequences of unknown significance in 1987 is fascinating, highly instructive, and inspiring for future advances in medicine. The recent approval of CRISPR-Cas9-based gene therapy to treat patients with severe sickle cell anemia and transfusion-dependent β-thalassemia has renewed hope for treating other hematologic diseases, including patients with a germline predisposition to hematologic malignancies, who would benefit greatly from the development of CRISPR-inspired gene therapies. The purpose of this paper is three-fold: first, a chronological description of the history of CRISPR-Cas9-sgRNA-based gene editing; second, a brief description of the current state of clinical research in hematologic diseases, including selected applications in treating hematologic diseases with CRISPR-based gene therapy, preceded by a brief description of the current tools being used in clinical genome editing; and third, a presentation of the current progress in gene therapies in inherited hematologic diseases and bone marrow failure syndromes, to hopefully stimulate efforts towards developing these therapies for patients with inherited bone marrow failure syndromes and other inherited conditions with a germline predisposition to hematologic malignancies.
Collapse
Affiliation(s)
- Rina Kansal
- Molecular Oncology and Genetics, Diagnostic Laboratories, Versiti Blood Center of Wisconsin, Milwaukee, WI 53233, USA;
- Department of Pathology and Anatomical Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| |
Collapse
|
33
|
He L, Li Z, Su D, Du H, Zhang K, Zhang W, Wang S, Xie F, Qiu Y, Ma S, Shi G, Yu D, Lei X, Li W, Li M, Wang Z, Gu J, Zhang Y. Tumor Microenvironment-Responsive Nanocapsule Delivery CRISPR/Cas9 to Reprogram the Immunosuppressive Microenvironment in Hepatoma Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403858. [PMID: 38704691 PMCID: PMC11234430 DOI: 10.1002/advs.202403858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Indexed: 05/07/2024]
Abstract
Cancer immunotherapy has demonstrated significant efficacy in various tumors, but its effectiveness in treating Hepatocellular Carcinoma (HCC) remains limited. Therefore, there is an urgent need to identify a new immunotherapy target and develop corresponding intervention strategies. Bioinformatics analysis has revealed that growth differentiation factor 15 (GDF15) is highly expressed in HCC and is closely related to poor prognosis of HCC patients. The previous study revealed that GDF15 can promote immunosuppression in the tumor microenvironment. Therefore, knocking out GDF15 through gene editing could potentially reverse the suppressive tumor immune microenvironment permanently. To deliver the CRISPR/Cas9 system specifically to HCC, nanocapsules (SNC) coated with HCC targeting peptides (SP94) on their surface is utilized. These nanocapsules incorporate disulfide bonds (SNCSS) that release their contents in the tumor microenvironment characterized by high levels of glutathione (GSH). In vivo, the SNCSS target HCC cells, exert a marked inhibitory effect on HCC progression, and promote HCC immunotherapy. Mechanistically, CyTOF analysis showed favorable changes in the immune microenvironment of HCC, immunocytes with killer function increased and immunocytes with inhibitive function decreased. These findings highlight the potential of the CRISPR-Cas9 gene editing system in modulating the immune microenvironment and improving the effectiveness of existing immunotherapy approaches for HCC.
Collapse
Affiliation(s)
- Lei He
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Zhaozhao Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Danjie Su
- Department of Obstetrics and GynecologyTangdu HospitalThe Fourth Military Medical UniversityXi'an710038China
| | - Haichen Du
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
- Department of Oncology940th HospitalJoint Logistic Support ForceLanzhou730050China
| | - Kuo Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Wangqian Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Shuning Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Fei Xie
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Yueyuan Qiu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Shuangxin Ma
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Gege Shi
- College of Life SciencesNorthwest UniversityXi'an710069China
| | - Duo Yu
- Department of NeurosurgeryGeneral Hospital of Central Theater CommandWuhan430012China
| | - Xiaoying Lei
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Weina Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Meng Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Zhaowei Wang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Jintao Gu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| | - Yingqi Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal CancersDepartment of BiopharmaceuticsSchool of PharmacyThe Fourth Military Medical UniversityXi'an710032China
| |
Collapse
|
34
|
Zhu Y, Lin Y, Gong B, Zhang Y, Su G, Yu Y. Dual toeholds regulated CRISPR-Cas12a sensing platform for ApoE single nucleotide polymorphisms genotyping. Biosens Bioelectron 2024; 255:116255. [PMID: 38565025 DOI: 10.1016/j.bios.2024.116255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Single nucleotide polymorphisms (SNPs) are closely associated with many biological processes, including genetic disease, tumorigenesis, and drug metabolism. Accurate and efficient SNP determination has been proved pivotal in pharmacogenomics and diagnostics. Herein, a universal and high-fidelity genotyping platform is established based on the dual toeholds regulated Cas12a sensing methodology. Different from the conventional single stranded or double stranded activation mode, the dual toeholds regulated mode overcomes protospacer adjacent motif (PAM) limitation via cascade toehold mediated strand displacement reaction, which is highly universal and ultra-specific. To enhance the sensitivity for biological samples analysis, a modified isothermal recombinant polymerase amplification (RPA) strategy is developed via utilizing deoxythymidine substituted primer and uracil-DNA glycosylase (UDG) treatment, designated as RPA-UDG. The dsDNA products containing single stranded toehold domain generated in the RPA-UDG allow further incorporation with dual toeholds regulated Cas12a platform for high-fidelity human sample genotyping. We discriminate all the single-nucleotide polymorphisms of ApoE gene at rs429358 and rs7412 loci with human buccal swab samples with 100% accuracy. Furthermore, we engineer visual readout of genotyping results by exploiting commercial lateral flow strips, which opens new possibilities for field deployable implementation.
Collapse
Affiliation(s)
- Yuedong Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yanan Lin
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Bin Gong
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yan Zhang
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
| |
Collapse
|
35
|
Xie G, Lu Y, He J, Yang X, Zhou J, Yi C, Li J, Li Z, Asadikaram G, Niu H, Xiong X, Li J, Wang H. Small Molecule-Inducible and Photoactivatable Cellular RNA N1-Methyladenosine Editing. Angew Chem Int Ed Engl 2024; 63:e202320029. [PMID: 38591694 DOI: 10.1002/anie.202320029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
N1-methyladenosine (m1A) modification is one of the most prevalent epigenetic modifications on RNA. Given the vital role of m1A modification in RNA processing such as splicing, stability and translation, developing a precise and controllable m1A editing tool is pivotal for in-depth investigating the biological functions of m1A. In this study, we developed an abscisic acid (ABA)-inducible and reversible m1A demethylation tool (termed AI-dm1A), which targets specific transcripts by combining the chemical proximity-induction techniques with the CRISPR/dCas13b system and ALKBH3. We successfully employed AI-dm1A to selectively demethylate the m1A modifications at A8422 of MALAT1 RNA, and this demethylation process could be reversed by removing ABA. Furthermore, we validated its demethylation function on various types of cellular RNAs including mRNA, rRNA and lncRNA. Additionally, we used AI-dm1A to specifically demethylate m1A on ATP5D mRNA, which promoted ATP5D expression and enhanced the glycolysis activity of tumor cells. Conversely, by replacing the demethylase ALKBH3 with methyltransferase TRMT61A, we also developed a controllable m1A methylation tool, namely AI-m1A. Finally, we caged ABA by 4,5-dimethoxy-2-nitrobenzyl (DMNB) to achieve light-inducible m1A methylation or demethylation on specific transcripts. Collectively, our m1A editing tool enables us to flexibly study how m1A modifications on specific transcript influence biological functions and phenotypes.
Collapse
Affiliation(s)
- Guoyou Xie
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yunqing Lu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jiaxin He
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xianyuan Yang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jiawang Zhou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Yi
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jian Li
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, Hunan, P. R. China
| | - Zigang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Gholamreza Asadikaram
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Medical University Campus, Kerman, Iran
| | - Hongxin Niu
- Special Medical Service Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofeng Xiong
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jiexin Li
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hongsheng Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| |
Collapse
|
36
|
Guizar P, Abdalla AL, Monette A, Davis K, Caballero RE, Niu M, Liu X, Ajibola O, Murooka TT, Liang C, Mouland AJ. An HIV-1 CRISPR-Cas9 membrane trafficking screen reveals a role for PICALM intersecting endolysosomes and immunity. iScience 2024; 27:110131. [PMID: 38957789 PMCID: PMC11217618 DOI: 10.1016/j.isci.2024.110131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/12/2023] [Accepted: 05/24/2024] [Indexed: 07/04/2024] Open
Abstract
HIV-1 hijacks host proteins involved in membrane trafficking, endocytosis, and autophagy that are critical for virus replication. Molecular details are lacking but are essential to inform on the development of alternative antiviral strategies. Despite their potential as clinical targets, only a few membrane trafficking proteins have been functionally characterized in HIV-1 replication. To further elucidate roles in HIV-1 replication, we performed a CRISPR-Cas9 screen on 140 membrane trafficking proteins. We identified phosphatidylinositol-binding clathrin assembly protein (PICALM) that influences not only infection dynamics but also CD4+ SupT1 biology. The knockout (KO) of PICALM inhibited viral entry. In CD4+ SupT1 T cells, KO cells exhibited defects in intracellular trafficking and increased abundance of intracellular Gag and significant alterations in autophagy, immune checkpoint PD-1 levels, and differentiation markers. Thus, PICALM modulates a variety of pathways that ultimately affect HIV-1 replication, underscoring the potential of PICALM as a future target to control HIV-1.
Collapse
Affiliation(s)
- Paola Guizar
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Ana Luiza Abdalla
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Anne Monette
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Kristin Davis
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Ramon Edwin Caballero
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Meijuan Niu
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Xinyun Liu
- Rady Faculty of Health Science, Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Oluwaseun Ajibola
- Rady Faculty of Health Science, Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Thomas T. Murooka
- Rady Faculty of Health Science, Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
- Rady Faculty of Health Science, Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Chen Liang
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Andrew J. Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| |
Collapse
|
37
|
Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. Cell 2024; 187:3249-3261.e14. [PMID: 38781968 DOI: 10.1016/j.cell.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/20/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.
Collapse
Affiliation(s)
- Amy R Eggers
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Owen T Tuck
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
38
|
Lee JC, Ryu SM, Lee Y, Jang H, Song J, Kang T, Lee KH, Park S. CRISPR/Cas12a antifouling nanocomposite electrochemical biosensors enable amplification-free detection of Monkeypox virus in complex biological fluids. NANOSCALE 2024; 16:11318-11326. [PMID: 38804270 DOI: 10.1039/d4nr01618a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The escalating global threat of infectious diseases, including monkeypox virus (MPXV), necessitates advancements in point-of-care diagnostics, moving beyond the constraints of conventional methods tethered to centralized laboratories. Here, we introduce multiple CRISPR RNA (crRNA)-based biosensors that can directly detect MPXV within 35 minutes without pre-amplification, leveraging the enhanced sensitivity and antifouling attributes of the BSA-based nanocomposite. Multiple crRNAs, strategically targeting diverse regions of the F3L gene of MPXV, are designed and combined to amplify Cas12a activation and its collateral cleavage of reporter probes. Notably, our electrochemical sensors exhibit the detection limit of 669 fM F3L gene without amplification, which is approximately a 15-fold improvement compared to fluorescence detection. This sensor also shows negligible changes in peak current after exposure to complex biological fluids, such as whole blood and serum, maintaining its sensitivity at 682 fM. This sensitivity is nearly identical to the conditions when only the F3L gene was present in PBS. In summary, our CRISPR-based electrochemical biosensors can be utilized as a high-performance diagnostic tool in resource-limited settings, representing a transformative leap forward in point-of-care testing. Beyond infectious diseases, the implications of this technology extend to various molecular diagnostics, establishing itself as a rapid, accurate, and versatile platform for detection of target analytes.
Collapse
Affiliation(s)
- Jeong-Chan Lee
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seuk-Min Ryu
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - YongJin Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Forensic Sciences, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Kwan Hyi Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| |
Collapse
|
39
|
Zhang L, Li K, Liu Z, An L, Wei H, Pang S, Cao Z, Huang X, Jin X, Ma X. Restoring T and B cell generation in X-linked severe combined immunodeficiency mice through hematopoietic stem cells adenine base editing. Mol Ther 2024; 32:1658-1671. [PMID: 38532630 PMCID: PMC11184316 DOI: 10.1016/j.ymthe.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/15/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
Base editing of hematopoietic stem/progenitor cells (HSPCs) is an attractive strategy for treating immunohematologic diseases. However, the feasibility of using adenine-base-edited HSPCs for treating X-linked severe combined immunodeficiency (SCID-X1), the influence of dose-response relationships on immune cell generation, and the potential risks have not been demonstrated in vivo. Here, a humanized SCID-X1 mouse model was established, and 86.67% ± 2.52% (n = 3) of mouse hematopoietic stem cell (HSC) pathogenic mutations were corrected, with no single-guide-RNA (sgRNA)-dependent off-target effects detected. Analysis of peripheral blood over 16 weeks post-transplantation in mice with different immunodeficiency backgrounds revealed efficient immune cell generation following transplantation of different amounts of modified HSCs. Therefore, a large-scale infusion of gene-corrected HSCs within a safe range can achieve rapid, stable, and durable immune cell regeneration. Tissue-section staining further demonstrated the restoration of immune organ tissue structures, with no tumor formation in multiple organs. Collectively, these data suggest that base-edited HSCs are a potential therapeutic approach for SCID-X1 and that a threshold infusion dose of gene-corrected cells is required for immune cell regeneration. This study lays a theoretical foundation for the clinical application of base-edited HSCs in treating SCID-X1.
Collapse
Affiliation(s)
- Lu Zhang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Haikun Wei
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Shanshan Pang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Zongfu Cao
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaohua Jin
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
| |
Collapse
|
40
|
Yang H, Patel DJ. Structures, mechanisms and applications of RNA-centric CRISPR-Cas13. Nat Chem Biol 2024; 20:673-688. [PMID: 38702571 DOI: 10.1038/s41589-024-01593-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
Prokaryotes are equipped with a variety of resistance strategies to survive frequent viral attacks or invading mobile genetic elements. Among these, CRISPR-Cas surveillance systems are abundant and have been studied extensively. This Review focuses on CRISPR-Cas type VI Cas13 systems that use single-subunit RNA-guided Cas endonucleases for targeting and subsequent degradation of foreign RNA, thereby providing adaptive immunity. Notably, distinct from single-subunit DNA-cleaving Cas9 and Cas12 systems, Cas13 exhibits target RNA-activated substrate RNase activity. This Review outlines structural, biochemical and cell biological studies toward elucidation of the unique structural and mechanistic principles underlying surveillance effector complex formation, precursor CRISPR RNA (pre-crRNA) processing, self-discrimination and RNA degradation in Cas13 systems as well as insights into suppression by bacteriophage-encoded anti-CRISPR proteins and regulation by endogenous accessory proteins. Owing to its programmable ability for RNA recognition and cleavage, Cas13 provides powerful RNA targeting, editing, detection and imaging platforms with emerging biotechnological and therapeutic applications.
Collapse
Affiliation(s)
- Hui Yang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
41
|
Yang S, Im SH, Chung JY, Lee J, Lee KH, Kang YK, Chung HJ. An Antibody-CRISPR/Cas Conjugate Platform for Target-Specific Delivery and Gene Editing in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308763. [PMID: 38552157 DOI: 10.1002/advs.202308763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/19/2024] [Indexed: 06/06/2024]
Abstract
The CRISPR/Cas system has been introduced as an innovative tool for therapy, however achieving specific delivery to the target has been a major challenge. Here, an antibody-CRISPR/Cas conjugate platform that enables specific delivery and target gene editing in HER2-positive cancer is introduced. The CRISPR/Cas system by replacing specific residues of Cas9 with an unnatural amino acid is engineered, that can be complexed with a nanocarrier and bioorthogonally functionalized with a monoclonal antibody targeting HER2. The resultant antibody-conjugated CRISPR/Cas nanocomplexes can be specifically delivered and induce gene editing in HER2-positive cancer cells in vitro. It is demonstrated that the in vivo delivery of the antibody-CRISPR/Cas nanocomplexes can effectively disrupt the plk1 gene in HER2-positive ovarian cancer, resulting in substantial suppression of tumor growth. The current study presents a useful therapeutic platform for antibody-mediated delivery of CRISPR/Cas for the treatment of various cancers and genetic diseases.
Collapse
Affiliation(s)
- Seungju Yang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - San Hae Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Ju Yeon Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Juhee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyung-Hun Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, 03080, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080, Republic of Korea
| | - Yoo Kyung Kang
- College of Pharmacy, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| |
Collapse
|
42
|
Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
Collapse
Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| |
Collapse
|
43
|
Bergman S, Tuller T. Strong association between genomic 3D structure and CRISPR cleavage efficiency. PLoS Comput Biol 2024; 20:e1012214. [PMID: 38848440 PMCID: PMC11189236 DOI: 10.1371/journal.pcbi.1012214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/20/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
CRISPR is a gene editing technology which enables precise in-vivo genome editing; but its potential is hampered by its relatively low specificity and sensitivity. Improving CRISPR's on-target and off-target effects requires a better understanding of its mechanism and determinants. Here we demonstrate, for the first time, the chromosomal 3D spatial structure's association with CRISPR's cleavage efficiency, and its predictive capabilities. We used high-resolution Hi-C data to estimate the 3D distance between different regions in the human genome and utilized these spatial properties to generate 3D-based features, characterizing each region's density. We evaluated these features based on empirical, in-vivo CRISPR efficiency data and compared them to 425 features used in state-of-the-art models. The 3D features ranked in the top 13% of the features, and significantly improved the predictive power of LASSO and xgboost models trained with these features. The features indicated that sites with lower spatial density demonstrated higher efficiency. Understanding how CRISPR is affected by the 3D DNA structure provides insight into CRISPR's mechanism in general and improves our ability to correctly predict CRISPR's cleavage as well as design sgRNAs for therapeutic and scientific use.
Collapse
Affiliation(s)
- Shaked Bergman
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| |
Collapse
|
44
|
Shi J, Lei C, Fan W, Sun Y, Liu C. Ultrasensitive protein and exosome analysis based on a rolling circle amplification assisted-CRISPR/Cas12a strategy. Talanta 2024; 273:125906. [PMID: 38490023 DOI: 10.1016/j.talanta.2024.125906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/15/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
CRISPR/Cas12a system has attracted extensive concern in biosensing due to its high specificity and programmability. Nevertheless, existing Cas12a-based assays mainly focus on nucleic acid detection and have limitations in non-nucleic acid biomarker analysis. To broaden the application prospect of the CRISPR/Cas technology, a cascade Cas12a biosensing platform is reported by combining dual-functionalized gold nanoparticles (FGNPs)-assisted rolling circle amplification (RCA) and Cas12a trans-cleavage activity (GAR-Cas) for ultrasensitive protein and exosome analysis. FGNPs serve as a critical component in the transduction of protein or exosome recognition information into nucleic acid amplification events to produce Cas12a activators. In the GAR-Cas assay, by integrating the triple cascade amplification of FGNPs-assisted transduction, RCA, and Cas12a signal amplification, ultralow abundance of target molecules can arouse numerous concatemers to activate Cas12a trans-cleavage activity to release intense fluorescence, allowing the ultrasensitive detection of as low as 1 fg/mL (∼41 aM) cTnI and 5 exosomes per μL. Furthermore, the presented strategy can be applied to detect exosome levels from clinical samples, showing excellent performance in distinguishing cancer patients from healthy individuals. The GAR-Cas sensing platform exhibits great potential in clinical diagnosis and enlarges biosensing toolboxes based on CRISPR/Cas technology for non-nucleic acid target analysis.
Collapse
Affiliation(s)
- Jingjing Shi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Yuanyuan Sun
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan Province, PR China.
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
| |
Collapse
|
45
|
Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
Collapse
Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
46
|
Palaz F, Ozsoz M, Zarrinpar A, Sahin I. CRISPR in Targeted Therapy and Adoptive T Cell Immunotherapy for Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:975-995. [PMID: 38832119 PMCID: PMC11146628 DOI: 10.2147/jhc.s456683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Despite recent therapeutic advancements, outcomes for advanced hepatocellular carcinoma (HCC) remain unsatisfactory, highlighting the need for novel treatments. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology offers innovative treatment approaches, involving genetic manipulation of either cancer cells or adoptive T cells to combat HCC. This review comprehensively assesses the applications of CRISPR systems in HCC treatment, focusing on in vivo targeting of cancer cells and the development of chimeric antigen receptor (CAR) T cells and T cell receptor (TCR)-engineered T cells. We explore potential synergies between CRISPR-based cancer therapeutics and existing treatment options, discussing ongoing clinical trials and the role of CRISPR technology in improving HCC treatment outcomes with advanced safety measures. In summary, this review provides insights into the promising prospects and current challenges of using CRISPR technology in HCC treatment, with the ultimate goal of improving patient outcomes and revolutionizing the landscape of HCC therapeutics.
Collapse
Affiliation(s)
- Fahreddin Palaz
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, Nicosia, Turkey
| | - Ali Zarrinpar
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Ilyas Sahin
- University of Florida Health Cancer Center, Gainesville, FL, USA
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
47
|
Dong J, Feng W, Lin M, Chen S, Liu X, Wang X, Chen Q. Comparative Evaluation of PCR-Based, LAMP and RPA-CRISPR/Cas12a Assays for the Rapid Detection of Diaporthe aspalathi. Int J Mol Sci 2024; 25:5773. [PMID: 38891961 PMCID: PMC11172161 DOI: 10.3390/ijms25115773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Southern stem canker (SSC) of soybean, attributable to the fungal pathogen Diaporthe aspalathi, results in considerable losses of soybean in the field and has damaged production in several of the main soybean-producing countries worldwide. Early and precise identification of the causal pathogen is imperative for effective disease management. In this study, we performed an RPA-CRISPR/Cas12a, as well as LAMP, PCR and real-time PCR assays to verify and compare their sensitivity, specificity and simplicity and the practicality of the reactions. We screened crRNAs targeting a specific single-copy gene, and optimized the reagent concentrations, incubation temperatures and times for the conventional PCR, real-time PCR, LAMP, RPA and Cas12a cleavage stages for the detection of D. aspalathi. In comparison with the PCR-based assays, two thermostatic detection technologies, LAMP and RPA-CRISPR/Cas12a, led to higher specificity and sensitivity. The sensitivity of the LAMP assay could reach 0.01 ng μL-1 genomic DNA, and was 10 times more sensitive than real-time PCR (0.1 ng μL-1) and 100 times more sensitive than conventional PCR assay (1.0 ng μL-1); the reaction was completed within 1 h. The sensitivity of the RPA-CRISPR/Cas12a assay reached 0.1 ng μL-1 genomic DNA, and was 10 times more sensitive than conventional PCR (1.0 ng μL-1), with a 30 min reaction time. Furthermore, the feasibility of the two thermostatic methods was validated using infected soybean leaf and seeding samples. The rapid, visual one-pot detection assay developed could be operated by non-expert personnel without specialized equipment. This study provides a valuable diagnostic platform for the on-site detection of SSC or for use in resource-limited areas.
Collapse
Affiliation(s)
- Jiali Dong
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Shuzhe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaozhen Liu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaodan Wang
- Sanya Institute of China Agricultural University, Sanya 572025, China;
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China; (J.D.); (W.F.); (M.L.); (S.C.); (X.L.)
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
| |
Collapse
|
48
|
Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
Collapse
Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| |
Collapse
|
49
|
Matsuda T, Hori H, Yamagami R. Rational design of oligonucleotides for enhanced in vitro transcription of small RNA. RNA (NEW YORK, N.Y.) 2024; 30:710-727. [PMID: 38423625 PMCID: PMC11098460 DOI: 10.1261/rna.079923.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
All kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR, or DNA cloning. The oligonucleotide design, however, is a challenge to nonexperts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the rational design of oligonucleotides, calculated with kinetic parameters for enhanced in vitro transcription (ROCKET). The Python tool uses thermodynamic parameters, performs folding-energy calculations, and selects oligonucleotides suitable for the polymerase extension reaction. These oligonucleotides improve yields of template DNA. With the oligonucleotides selected by the program, the tRNA transcripts can be prepared by a one-pot reaction of the DNA polymerase extension reaction and the transcription reaction. Also, the ROCKET-selected oligonucleotides provide greater transcription yields than that from oligonucleotides selected by Primerize, a leading software for designing oligonucleotides for in vitro transcription, due to the enhancement of template DNA synthesis. Apart from over 50 tRNA genes tested, an in vitro transcribed self-cleaving ribozyme was found to have catalytic activity. In addition, the program can be applied to the synthesis of mRNA, demonstrating the wide applicability of the ROCKET software.
Collapse
MESH Headings
- Transcription, Genetic
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/chemical synthesis
- Software
- DNA-Directed RNA Polymerases/metabolism
- DNA-Directed RNA Polymerases/genetics
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/chemistry
- Thermodynamics
- RNA, Transfer/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Kinetics
- RNA, Messenger/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Viral Proteins/genetics
- Viral Proteins/metabolism
Collapse
Affiliation(s)
- Teppei Matsuda
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
50
|
Bhattacharya S, Agarwal A, Muniyappa K. Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities. J Mol Biol 2024; 436:168550. [PMID: 38575054 DOI: 10.1016/j.jmb.2024.168550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
Collapse
Affiliation(s)
- Supreet Bhattacharya
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
| |
Collapse
|