201
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Kuhns S, Juhl AD, Anvarian Z, Wüstner D, Pedersen LB, Andersen JS. Endogenous Tagging of Ciliary Genes in Human RPE1 Cells for Live-Cell Imaging. Methods Mol Biol 2024; 2725:147-166. [PMID: 37856023 DOI: 10.1007/978-1-0716-3507-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
CRISPR-mediated endogenous tagging of genes provides unique possibilities to explore the function and dynamic subcellular localization of proteins in living cells. Here, we describe experimental strategies for endogenous PCR-tagging of ciliary genes in human RPE1 cells and how image acquisition and analysis of the expressed fluorescently tagged proteins can be utilized to study the dynamic ciliary processes of intraflagellar transport and vesicular trafficking.
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Affiliation(s)
- Stefanie Kuhns
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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202
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Nie X, Wang D, Pan Y, Hua Y, Lü P, Yang Y. Discovery, classification and application of the CPISPR-Cas13 system. Technol Health Care 2024; 32:525-544. [PMID: 37545273 DOI: 10.3233/thc-230258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins. OBJECTIVE This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance. METHODS Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed. RESULTS The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA. CONCLUSION The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.
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Affiliation(s)
- Xiaojuan Nie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Pan
- School of Experimental Animal Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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203
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Rivera J, Mu Y, Gordon CA, Jones MK, Cheng G, Cai P. Current and upcoming point-of-care diagnostics for schistosomiasis. Trends Parasitol 2024; 40:60-74. [PMID: 38000956 DOI: 10.1016/j.pt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
Point-of-care (POC) diagnostics are simple and effective portable tools that can be used for fast mapping of helminthic diseases and monitoring control programs. Most POC tests (POCTs) available for schistosomiasis diagnosis are lateral flow immunoassays (LFIAs). The emergence of simple and rapid DNA isolation methods, along with isothermal nucleic acid amplification strategies - for example, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) - and recent clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic methods facilitate the development of molecular-based POC diagnostics for schistosomiasis. Furthermore, smartphone-based techniques increase real-time connectivity and readout accuracy of POCTs. This review discusses the recent advances in immunological-, molecular-based POCTs and mobile phone microscopes for the diagnosis/screening of schistosomiasis.
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Affiliation(s)
- Jonas Rivera
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Yi Mu
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Malcolm K Jones
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - Guofeng Cheng
- Shanghai Tenth People's Hospital, Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, Australia.
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204
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Ray SK, Mukherjee S. Innovation and Patenting Activities During COVID-19 and Advancement of Biochemical and Molecular Diagnosis in the Post- COVID-19 Era. Recent Pat Biotechnol 2024; 18:210-226. [PMID: 37779409 DOI: 10.2174/0118722083262217230921042127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 10/03/2023]
Abstract
The COVID-19 pandemic is to escalate globally and acquire new mutations quickly, so accurate diagnostic technologies play a vital role in controlling and understanding the epidemiology of the disease. A plethora of technologies acquires diagnosis of individuals and informs clinical management of COVID. Some important biochemical parameters for COVID diagnosis are the elevation of liver enzymes, creatinine, and nonspecific inflammatory markers such as C-reactive protein (CRP) and Interleukin 6 (IL-6). The main progression predictors are lymphopenia, elevated D-dimer, and hyperferritinemia, although it is also necessary to consider LDH, CPK, and troponin in the marker panel of diagnosis. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively used for COVID diagnosis for some time now. To make so many diagnostics accessible to general people, many techniques may be exploited, including point of care (POC), also called bedside testing, which is developing as a portable promising tool in pathogen identification. Some other lateral flow assay (LFA)-centered techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor limited uniform detection assay (FELUDA), etc. have shown auspicious results in the rapid detection of pathogens. More recently, low-cost sequencing and advancements in big data management have resulted in a slow but steady rise of next-generation sequencing (NGS)-based approaches for diagnosis that have potential relevance for clinical purposes and may pave the way toward a better future. Due to the COVID-19 pandemic, various institutions provided free, specialized websites and tools to promote research and access to critically needed advanced solutions by alleviating research and analysis of data within a substantial body of scientific and patent literature regarding biochemical and molecular diagnosis published since January 2020. This circumstance is unquestionably unique and difficult for anyone using patent information to find pertinent disclosures at a specific date in a trustworthy manner.
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Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
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205
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Kajuluri LP, Lyu QR, Doja J, Kumar A, Wilson MP, Sgrizzi SR, Rezaeimanesh E, Miano JM, Morgan KG. Calponin 1 inhibits agonist-induced ERK activation and decreases calcium sensitization in vascular smooth muscle. J Cell Mol Med 2024; 28:e18025. [PMID: 38147352 PMCID: PMC10805486 DOI: 10.1111/jcmm.18025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/07/2023] [Indexed: 12/27/2023] Open
Abstract
Smooth muscle cell (SMC) contraction and vascular tone are modulated by phosphorylation and multiple modifications of the thick filament, and thin filament regulation of SMC contraction has been reported to involve extracellular regulated kinase (ERK). Previous studies in ferrets suggest that the actin-binding protein, calponin 1 (CNN1), acts as a scaffold linking protein kinase C (PKC), Raf, MEK and ERK, promoting PKC-dependent ERK activation. To gain further insight into this function of CNN1 in ERK activation and the regulation of SMC contractility in mice, we generated a novel Calponin 1 knockout mouse (Cnn1 KO) by a single base substitution in an intronic CArG box that preferentially abolishes expression of CNN1 in vascular SMCs. Using this new Cnn1 KO mouse, we show that ablation of CNN1 has two effects, depending on the cytosolic free calcium level: (1) in the presence of elevated intracellular calcium caused by agonist stimulation, Cnn1 KO mice display a reduced amplitude of stress and stiffness but an increase in agonist-induced ERK activation; and (2) during intracellular calcium depletion, in the presence of an agonist, Cnn1 KO mice exhibit increased duration of SM tone maintenance. Together, these results suggest that CNN1 plays an important and complex modulatory role in SMC contractile tone amplitude and maintenance.
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Affiliation(s)
- Lova Prasadareddy Kajuluri
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
- Present address:
Cardiovascular Research CenterMassachusetts General HospitalCharlestownMassachusettsUSA
| | - Qing Rex Lyu
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
- Medical Research CenterChongqing General HospitalChongqingChina
| | - Jaser Doja
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | - Ajay Kumar
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | | | - Samantha R. Sgrizzi
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
| | - Elika Rezaeimanesh
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
| | - Joseph M. Miano
- Vascular Biology CenterMedical College of Georgia at Augusta UniversityAugustaGeorgiaUSA
| | - Kathleen G. Morgan
- Vascular Biology Laboratory, Department of Health SciencesBoston UniversityBostonMassachusettsUSA
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206
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Abasi F, Raja NI, Mashwani ZUR, Ehsan M, Ali H, Shahbaz M. Heat and Wheat: Adaptation strategies with respect to heat shock proteins and antioxidant potential; an era of climate change. Int J Biol Macromol 2024; 256:128379. [PMID: 38000583 DOI: 10.1016/j.ijbiomac.2023.128379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Extreme changes in weather including heat-wave and high-temperature fluctuations are predicted to increase in intensity and duration due to climate change. Wheat being a major staple crop is under severe threat of heat stress especially during the grain-filling stage. Widespread food insecurity underscores the critical need to comprehend crop responses to forthcoming climatic shifts, pivotal for devising adaptive strategies ensuring sustainable crop productivity. This review addresses insights concerning antioxidant, physiological, molecular impacts, tolerance mechanisms, and nanotechnology-based strategies and how wheat copes with heat stress at the reproductive stage. In this study stress resilience strategies were documented for sustainable grain production under heat stress at reproductive stage. Additionally, the mechanisms of heat resilience including gene expression, nanomaterials that trigger transcription factors, (HSPs) during stress, and physiological and antioxidant traits were explored. The most reliable method to improve plant resilience to heat stress must include nano-biotechnology-based strategies, such as the adoption of nano-fertilizers in climate-smart practices and the use of advanced molecular approaches. Notably, the novel resistance genes through advanced molecular approach and nanomaterials exhibit promise for incorporation into wheat cultivars, conferring resilience against imminent adverse environmental conditions. This review will help scientific communities in thermo-tolerance wheat cultivars and new emerging strategies to mitigate the deleterious impact of heat stress.
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Affiliation(s)
- Fozia Abasi
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan.
| | - Naveed Iqbal Raja
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan.
| | | | - Maria Ehsan
- Department of Botany, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Habib Ali
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Muhammad Shahbaz
- Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, 88400 Kota Kinabalu, Malaysia
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207
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Abstract
In this review, we detail the current state of application of gene therapy to primary mitochondrial disorders (PMDs). Recombinant adeno-associated virus-based (rAAV) gene replacement approaches for nuclear gene disorders have been undertaken successfully in more than ten preclinical mouse models of PMDs which has been made possible by the development of novel rAAV technologies that achieve more efficient organ targeting. So far, however, the greatest progress has been made for Leber Hereditary Optic Neuropathy, for which phase 3 clinical trials of lenadogene nolparvovec demonstrated efficacy and good tolerability. Other methods of treating mitochondrial DNA (mtDNA) disorders have also had traction, including refinements to nucleases that degrade mtDNA molecules with pathogenic variants, including transcription activator-like effector nucleases, zinc-finger nucleases, and meganucleases (mitoARCUS). rAAV-based approaches have been used successfully to deliver these nucleases in vivo in mice. Exciting developments in CRISPR-Cas9 gene editing technology have achieved in vivo gene editing in mouse models of PMDs due to nuclear gene defects and new CRISPR-free gene editing approaches have shown great potential for therapeutic application in mtDNA disorders. We conclude the review by discussing the challenges of translating gene therapy in patients both from the point of view of achieving adequate organ transduction as well as clinical trial design.
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Affiliation(s)
- Nandaki Keshavan
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital, London, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Shamima Rahman
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital, London, UK
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208
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Misra G, Qaisar S, Singh P. CRISPR-based therapeutic targeting of signaling pathways in breast cancer. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166872. [PMID: 37666438 DOI: 10.1016/j.bbadis.2023.166872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Breast cancer remains a leading cause of death for women worldwide, and new treatment strategies are needed. There are innumerable anomalous genes that are responsible for the multi-factorial carcinogenesis pathway. Although several disease-causing mutations have been detected, therapy frequently focuses on attenuating the manifestation of the disease rather than harmonizing the mutation in the target area. The advent of CRISPR-Cas9 technology has revolutionized genome editing, allowing for precise and efficient manipulation of gene expression. The purpose of this review paper is to summarize recent progress in the use of CRISPR-based approaches to target key signaling pathways associated with breast cancer progression. The first section introduces basic concepts of CRISPR technology, focusing on its application in genome editing and transcriptional regulation followed by an overview of aspects involving complex signaling pathways in breast cancer such as P13K/AKT/mTOR, EPK/MAPK and Wnt/β catenin. An extensive literature search using PubMed and Google Scholar is performed for information retrieval. Further, the role of CRISPR-based interventions in regulating gene expression revealed, altered pathway activity and potential therapeutic consequences are discussed. This review will be a valuable addition to providing comprehensive knowledge of CRISPR-Cas-mediated therapeutic targeting in breast cancer.
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Affiliation(s)
- Gauri Misra
- National Institute of Biologicals, Noida 201309, UP, India.
| | - Sidra Qaisar
- National Institute of Biologicals, Noida 201309, UP, India
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209
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Freen-van Heeren JJ. Employing CRISPR-Cas9 to Enhance T Cell Effector Function. Methods Mol Biol 2024; 2782:195-208. [PMID: 38622404 DOI: 10.1007/978-1-0716-3754-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
As part of the adaptive immune system, T cells are critical to maintain immune homeostasis. T cells provide protective immunity by killing infected cells and combatting cancerous cells. To do so, T cells produce and secrete effector molecules, such as granzymes, perforin, and cytokines such as tumor necrosis factor α and interferon γ. However, in immune suppressive environments, such as tumors, T cells gradually lose the capacity to perform their effector function. One way T cell effector function can be enhanced is through genetic engineering with tools such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9). This protocol explains in a step-by-step fashion how to perform a controlled electroporation-based CRISPR experiment to enhance human T cell effector function. Of note, these steps are suitable for CRISPR-mediated genome editing in T cells in general and can thus also be used to study proteins of interest that do not influence T cell effector function.
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210
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Stanley SM, Khera HK, Chandrasingh S, George CE, Mishra RK. A comprehensive review of dengue with a focus on emerging solutions for precision and timely detection. Int J Biol Macromol 2024; 254:127613. [PMID: 37875186 DOI: 10.1016/j.ijbiomac.2023.127613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
Dengue is a global health problem, caused by the dengue virus (DENV), which belongs to the Flaviviridae family of viruses. The transmission of DENV occurs through vectors, Ae. aegypti and Ae. Albopictus mosquitoes, to the human host, classifying it as a vector-borne disease. The disease incidence is increasing at an alarming rate and needs to be tackled to reduce the morbidity and mortality caused by the disease. Environmental and clinical surveillance, detection of the virus, and diagnostics are critical tools to address this issue. In this comprehensive review, we explore various diagnostic techniques and the associated challenges within the context of dengue. While we briefly touch upon dengue's epidemiology, serotypes, and pathogenesis, our primary emphasis remains on diagnostics. We delve into the intricacies of these diagnostic methods, considering both the challenges they entail and the potential they hold in terms of accuracy and accessibility. It's important to note that the review does not extensively cover clinical aspects or regional variations of the disease.
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Affiliation(s)
- Swetha Mariam Stanley
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India
| | - Harvinder Kour Khera
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India.
| | | | | | - Rakesh K Mishra
- Tata Institute for Genetics and Society, Bangalore Life Science Cluster (BLiSC), inStem Building, NCBS Campus, GKVK Post, Bellary Road, Bengaluru, India
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211
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Heu CC, Le KP, Gross RJ, Schutze IX, LeRoy DM, Langhorst D, Brent CS, Fabrick JA, Hull JJ. β-tubulin functions in spermatogenesis in Lygus hesperus Knight. J Insect Physiol 2024; 152:104598. [PMID: 38081537 DOI: 10.1016/j.jinsphys.2023.104598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Lygus hesperus Knight is an important insect pest of crops across western North America, with field management heavily reliant on the use of chemical insecticides. Because of the evolution of resistance to these insecticides, effective and environmentally benign pest management strategies are needed. Traditional sterile insect technique (SIT) has been successfully employed to manage or eradicate some insect pests but involves introducing irradiated insects with random mutations into field populations. New genetically-driven SIT techniques are a safer alternative, causing fixed mutations that manipulate individual genes in target pests to produce sterile individuals for release. Here, we identified seven β-tubulin coding genes from L. hesperus and show that Lhβtub2 is critical in male sperm production and fertility. Lhβtub2 is expressed primarily in the male testes and targeting of this gene by RNA interference or gene editing leads to male sterility.
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Affiliation(s)
- Chan C Heu
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Kevin P Le
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Roni J Gross
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Inana X Schutze
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Dannialle M LeRoy
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Daniel Langhorst
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Colin S Brent
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - Jeffrey A Fabrick
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA
| | - J Joe Hull
- USDA ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ 85138 USA.
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212
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Reuven N, Barnea-Zohar M, Elson A. Osteoclast Methods in Protein Phosphatase Research. Methods Mol Biol 2024; 2743:57-79. [PMID: 38147208 DOI: 10.1007/978-1-0716-3569-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Osteoclasts are specialized cells that degrade bone and are essential for bone formation and maintaining bone homeostasis. Excess or deficient activity of these cells can significantly alter bone mass, structure, and physical strength, leading to significant morbidity, as in osteoporosis or osteopetrosis, among many other diseases. Protein phosphorylation in osteoclasts plays critical roles in the signaling pathways that govern the production of osteoclasts and regulate their bone-resorbing activity. In this chapter, we describe the isolation of mouse splenocytes and their differentiation into mature osteoclasts on resorptive (e.g., bone) and non-resorptive (e.g., plastic or glass) surfaces, examining matrix resorption by osteoclasts, immunofluorescence staining of these cells, and knocking out genes by CRISPR in the mouse osteoclastogenic cell line RAW264.7.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Maayan Barnea-Zohar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel.
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213
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Pacia DM, Brown BL, Minssen T, Darrow JJ. CRISPR-phage antibacterials to address the antibiotic resistance crisis: scientific, economic, and regulatory considerations. J Law Biosci 2024; 11:lsad030. [PMID: 38283616 PMCID: PMC10817822 DOI: 10.1093/jlb/lsad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/22/2023] [Indexed: 01/30/2024]
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214
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Chung T, Merrill JR, Lyons SK. CRISPR/Cas for PET Reporter Gene Engineering. Methods Mol Biol 2024; 2729:285-301. [PMID: 38006503 DOI: 10.1007/978-1-0716-3499-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
The relatively recent discovery of CRISPR/Cas has led to a revolution in our ability to efficiently manipulate the genome of eukaryotic cells. We describe here a protocol that employs CRISPR technology to precisely knock-in a PET imaging reporter transgene into a specific genetic locus of interest. Resulting transcription of the targeted reporter will more accurately mimic physiologic expression of the endogenous allele than conventional approaches, and so this method has the potential to become an efficient way to generate a new generation of "gold-standard" reporter transgenes. We break down the protocol into three experimental stages: how to identify the genomic location that the reporter transgene will be inserted, how to practically insert the reporter transgene into the genome, and how to screen resultant clones for the correct targeted event.
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Affiliation(s)
- Taemoon Chung
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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215
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Huang LT, Colville MJ, Paszek M. Recombinant Production of Glycoengineered Mucins in HEK293-F Cells. Methods Mol Biol 2024; 2763:281-308. [PMID: 38347419 DOI: 10.1007/978-1-0716-3670-1_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Recombinant mucins are attractive polymeric building blocks for new biomaterials, biolubricants, and therapeutics. Advances in glycoengineered host cell systems now enable the recombinant production of mucins with tailored O-glycan side chains, offering new opportunities to tune the functionality of mucins and investigate the biology of specific O-glycan structures. Here, we provide a protocol for the scalable production of glycoengineered mucins and mucin-like glycoproteins in suspension-adapted HEK293-F cells. The protocol includes the preparation of engineered cell lines with homozygous knockout (KO) of glycosyltransferases using CRISPR/Cas9 and homology-directed repair (HDR) templates designed for efficient screening of clones. Strategies are provided for the stable introduction of mucin expression cassettes into the HEK293-F genome and the subsequent isolation of high-expressing cell populations. The high-titer production of recombinant mucins in conventional shaker flasks is described as an example production strategy using these cell lines.
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Affiliation(s)
- Ling-Ting Huang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Marshall J Colville
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matthew Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA
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216
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Shashank PR, Parker BM, Rananaware SR, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK, Kawahara AY. CRISPR-based diagnostics detects invasive insect pests. Mol Ecol Resour 2024; 24:e13881. [PMID: 37888995 PMCID: PMC10842307 DOI: 10.1111/1755-0998.13881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Rapid identification of organisms is essential for many biological and medical disciplines, from understanding basic ecosystem processes, disease diagnosis, to the detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than real-time PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a sophisticated laboratory, reduces the risk of cross-contamination, and can be completed in less than 1 h. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.
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Affiliation(s)
- Pathour R Shashank
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Division of Entomology, ICAR-Indian Agricultural Research Institution, New Delhi, India
| | - Brandon M Parker
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Santosh R Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Christian Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Lilia G Yang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - N R Prasannakumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - W Evan Braswell
- Insect Management and Molecular Diagnostics Laboratory, USDA APHIS PPQ S&T, Edinburg, Texas, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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217
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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218
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Zheng M, Zhang M, Li H, Wu S, Zhao Y, Zhang J, Zhou Y, Jalloh MB, Zhang K, Chen L, Mi Z, Cui Y, Hou L. Rapid, sensitive, and convenient detection of Plasmodium falciparum infection based on CRISPR and its application in detection of asymptomatic infection. Acta Trop 2024; 249:107062. [PMID: 37923286 DOI: 10.1016/j.actatropica.2023.107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Rapid and convenient detection of the Plasmodium in clinically diagnosed individuals and asymptomatically infected populations is essential for global malaria eradication, especially in malaria-endemic African countries where medical equipment and professionals are relatively deficient. Here, we described a CRISPR-based diagnostic for the detection of Plasmodium falciparum, the deadliest and most prevalent species of malaria parasite in Africa, via lateral flow strip readout without the need of nucleic acid extraction. The assay exhibited 100% sensitivity on clinical samples (5 P falciparum) and significant consistency with qPCR test on asymptomatic infection samples (49 P falciparum and 51 non-P. falciparum, Kappa=0.839). An artemisinin-resistant P. falciparum strain and 4 other laboratory-cultured strains can also be detected through this assay, whereas no cross-reactivity with Plasmodium vivax was observed. A 0.001% parasitaemia (corresponding to ∼60 parasites/μL) below the "low parasite density" test threshold (200 parasites/µL) is detectable. Our study demonstrated that direct malaria detection using whole blood on the spot and the detection of both clinical and asymptomatic infections of P. falciparum are feasible. This method is expected to be employed for clinical testing and large-scale community screening in Africa and possibly other places, contributing to the accurate diagnosis and control of malaria.
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Affiliation(s)
- Minghao Zheng
- School of Medical Devices, Shenyang Pharmaceutical University; Beijing Institute of Biotechnology, Beijing, China
| | | | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shipo Wu
- Beijing Institute of Biotechnology, Beijing, China
| | - Yuee Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | | | - Yunyue Zhou
- Beijing Institute of Biotechnology, Beijing, China; School of Basic Medical Sciences, Zhejiang University
| | - Mohamed Boie Jalloh
- Joint Medical Unit (34 Military Hospital), Republic of Sierra Leone Armed Forces, Wilberforce Barracks, Wilberforce Village, Freetown, Sierra Leone
| | - Kun Zhang
- Department of Cell Biology, National Translational Science Center for Molecular Medicine, Fourth Military Medical University
| | - Lina Chen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Yong Cui
- School of Medical Devices, Shenyang Pharmaceutical University.
| | - Lihua Hou
- Beijing Institute of Biotechnology, Beijing, China.
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219
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Cavanaugh C, Hesson J, Mathieu J. Genomic Engineering of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Methods Mol Biol 2024; 2735:129-143. [PMID: 38038847 DOI: 10.1007/978-1-0716-3527-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Recent advances in patient-derived induced Pluripotent Stem Cell (iPSC) generation, improvement of cardiomyocyte-directed differentiation protocols, and the availability of new genome editing techniques have opened up new avenues for disease modeling of cardiomyopathies. Patients with cardiomyopathies often harbor a single-base substitution believed to be linked to the disease phenotype. Somatic cells derived from patients can be efficiently reprogrammed into iPSCs and subsequently engineered. The targeting of a precise mutation can be achieved by the introduction of double stranded breaks with CRISPR-Cas9 and by homology-directed repair when using a DNA donor template. This allows for the correction of a mutation in a patient iPSC line to generate an isogenic control. In addition, key mutations associated with cardiomyopathies can be introduced in an iPSC line derived from a healthy individual using the same techniques. In this chapter, we describe in detail how to engineer pluripotent stem cells to model cardiomyopathy in a dish using CRISPR-Cas9 technology.
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Affiliation(s)
- Christopher Cavanaugh
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA
| | - Jennifer Hesson
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA
| | - Julie Mathieu
- Department of Comparative Medicine, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA.
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220
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Ravagnan G, Meliawati M, Schmid J. CRISPR-Cas9-Mediated Genome Editing in Paenibacillus polymyxa. Methods Mol Biol 2024; 2760:267-280. [PMID: 38468094 DOI: 10.1007/978-1-0716-3658-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
In recent years, the clustered regularly interspaced palindromic repeats-Cas (CRISPR-Cas) technology has become the method of choice for precision genome editing in many organisms due to its simplicity and efficacy. Multiplex genome editing, point mutations, and large genomic modifications are attractive features of the CRISPR-Cas9 system. These applications facilitate both the ease and velocity of genetic manipulations and the discovery of novel functions. In this protocol chapter, we describe the use of a CRISPR-Cas9 system for multiplex integration and deletion modifications, and deletions of large genomic regions by the use of a single guide RNA (sgRNA), and, finally, targeted point mutation modifications in Paenibacillus polymyxa.
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Affiliation(s)
- Giulia Ravagnan
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Meliawati Meliawati
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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221
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Monteiro M, Zhang X, Yee D. Insulin promotes growth in breast cancer cells through the type I IGF receptor in insulin receptor deficient cells. Exp Cell Res 2024; 434:113862. [PMID: 38036052 PMCID: PMC10842809 DOI: 10.1016/j.yexcr.2023.113862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Breast cancer is the most common cancer in women. The upregulation of insulin-like growth factor (IGF) system observed in certain types of breast cancers was linked to growth, metastasis, and survival resulting in multiple strategies designed to target the type I IGF receptor (IGF-1R) in breast cancer. These attempts failed to prove beneficial and it has been suggested that insulin receptor (IR) could also play an important role in breast cancer biology. To better understand the IR's role in breast cancer cells, the receptor was deleted from MCF-7L cells using CRISPR technology, and fluorescence-assisted cell sorting was used to obtain clone 35 (CL35). It was found that CL35 activated signaling pathways upon insulin stimulation despite the absence of IR expression. We hypothesized that CL35 used a surrogate receptor for sustained growth and development. IGF-1R was able to activate insulin signaling and growth in CL35. Thus, insulin may play a central role in regulating breast cancer growth due to its ability to activate all the receptors of the IGF family. These findings argue that dual targeting of IR and IGF-IR may be required to inhibit breast cancer growth.
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Affiliation(s)
- Marvis Monteiro
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA; Purdue University, Heine Pharmacy Building, 575 Stadium Mall Drive, West Lafayette, IN, 47907-2091, USA
| | - Xihong Zhang
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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222
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Rahman S, Ikram AR, Azeem F, Tahir Ul Qamar M, Shaheen T, Mehboob-Ur-Rahman. Precision Genome Editing with CRISPR-Cas9. Methods Mol Biol 2024; 2788:355-372. [PMID: 38656525 DOI: 10.1007/978-1-0716-3782-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The CRISPR/Cas9 system is a revolutionary technology for genome editing that allows for precise and efficient modifications of DNA sequences. The system is composed of two main components, the Cas9 enzyme and a guide RNA (gRNA). The gRNA is designed to specifically target a desired DNA sequence, while the Cas9 enzyme acts as molecular scissors to cut the DNA at that specific location. The cell then repairs the digested DNA, either through nonhomologous end joining (NHEJ) or homology-directed repair (HDR), resulting in either indels or precise modifications of DNA sequences with broad implications in biotechnology, agriculture, and medicine. This chapter provides a practical approach for utilizing CRISPR/Cas9 in precise genome editing, including identifying the target gene sequence, designing gRNA and protein (Cas9), and delivering the CRISPR components to target cells.
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Affiliation(s)
- Shahroz Rahman
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abdul Rehman Ikram
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Tayyaba Shaheen
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
| | - Mehboob-Ur-Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan.
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223
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Lee DS, Cho EJ, Nguyen DT, Song Y, Chang J, Bae HJ. Succinic acid production from softwood with genome-edited Corynebacterium glutamicum using the CRISPR-Cpf1 system. Biotechnol J 2024; 19:e2300309. [PMID: 38180273 DOI: 10.1002/biot.202300309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024]
Abstract
Corynebacterium glutamicum is a useful microbe that can be used for producing succinic acid under anaerobic conditions. In this study, we generated a knock-out mutant of the lactate dehydrogenase 1 gene (ΔldhA-6) and co-expressed the succinic acid transporter (Psod:SucE- ΔldhA) using the CRISPR-Cpf1 genome editing system. The highly efficient HPAC (hydrogen peroxide and acetic acid) pretreatment method was employed for the enzymatic hydrolysis of softwood (Pinus densiflora) and subsequently utilized for production of succinic acid. Upon evaluating a 1%-5% hydrolysate concentration range, optimal succinic acid production with the ΔldhA mutant was achieved at a 4% hydrolysate concentration. This resulted in 14.82 g L-1 succinic acid production over 6 h. No production of acetic acid and lactic acid was detected during the fermentation. The co-expression transformant, [Psod:SucE-ΔldhA] produced 17.70 g L-1 succinic acid in 6 h. In the fed-batch system, 39.67 g L-1 succinic acid was produced over 48 h. During the fermentation, the strain consumed 100% and 73% of glucose and xylose, respectively. The yield of succinic acid from the sugars consumed was approximately 0.77 g succinic acid/g sugars. These results indicate that the production of succinic acid from softwood holds potential applications in alternative biochemical processes.
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Affiliation(s)
- Dae-Seok Lee
- Bio-energy Research Institute, Chonnam National University, Gwangju, Republic of Korea
| | - Eun Jin Cho
- Bio-energy Research Institute, Chonnam National University, Gwangju, Republic of Korea
| | | | - Younho Song
- Bio-energy Research Institute, Chonnam National University, Gwangju, Republic of Korea
| | - Jihye Chang
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Hyeun-Jong Bae
- Bio-energy Research Institute, Chonnam National University, Gwangju, Republic of Korea
- School of Biotechology, Tan Tao University, Long An, Viet Nam
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224
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Goerlich CE, Kamberi SS, Ladowski J, Citro A, Connolly M, Fischer K, Salvaris EJ, Singh AK, Wang Y, Stern J, Meier RPH. The Young Investigator Committee of the International Xenotransplantation Association-Perspective of advancements in the field in 2023. Xenotransplantation 2024; 31:e12845. [PMID: 38407937 DOI: 10.1111/xen.12845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Abstract
The 2023 IXA conference, hosted in San Diego, CA, brimmed with excitement against the backdrop of recent innovations in both the pre-clinical and clinical realms with several first-in-human applications of xenotransplantation. The theme, "Pigs are flying," alluded to the adage that xenotransplantation would only become a clinical reality "when pigs fly," suggesting a day that might never come. The event witnessed significant attendance, with 600 participants-the highest in the history of an IXA-IPITA joint congress. Among the attendees were members of the Food and Drug Administration (FDA), the National Institutes of Health (NIH), and corporate sponsors deeply engaged in the field. We summarize the latest topics from the congress, ranging from the pros/cons of decedent models of xenotransplantation and genetic engineering of porcine heart valves, solid organs, and cells for clinical translation and their regulatory and ethical landscape.
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Affiliation(s)
- Corbin E Goerlich
- Department of Surgery, The University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Shani S Kamberi
- Department of Surgery, The University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Joseph Ladowski
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Antonio Citro
- San Raffaele Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Margaret Connolly
- Department of Surgery, Division of Cardiac Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Konrad Fischer
- School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Evelyn J Salvaris
- Immunology Research Centre, St. Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
| | - Avneesh K Singh
- Department of Surgery, The University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital & Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jeffrey Stern
- Transplant Institute, NYU Langone Health, New York, New York, USA
| | - Raphael P H Meier
- Department of Surgery, The University of Maryland School of Medicine, Baltimore, Maryland, USA
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225
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Huang S, Carter-Cusack D, Maxwell E, Patkar OL, Irvine KM, Hume DA. Genetic and Immunohistochemistry Tools to Visualize Rat Macrophages In Situ. Methods Mol Biol 2024; 2713:99-115. [PMID: 37639117 DOI: 10.1007/978-1-0716-3437-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Macrophages contribute to many aspects of development and homeostasis, innate and acquired immunity, immunopathology, and tissue repair. Every tissue contains an abundant resident macrophage population. Inflammatory stimuli promote the recruitment of monocytes from the blood and their adaptation promotes the removal of the stimulus and subsequent restoration of normal tissue architecture. Dysregulation of this response leads to chronic inflammation and tissue injury. In many tissues, their differentiation and survival are dependent on the colony stimulating factor 1 receptor (CSF1R) signalling axis, which is highly conserved across all vertebrates. Complete loss of either CSF1R or its cognate ligands, colony stimulating factor 1 (CSF1), and interleukin 34 (IL-34), results in the loss of many tissue-resident macrophage populations. This provides a useful paradigm to study macrophages.There are many tools used to visualize tissue-resident macrophages and their precursors, monocytes, in mice and humans. Particularly in mice there are genetic tools available to delete, enhance and manipulate monocytes and macrophages and their gene products to gain insight into phenotype and function. The laboratory rat has many advantages as an experimental model for the understanding of human disease, but the analytical resources are currently more limited than in mice. Here, we describe available genetic models, antibodies, and immunohistochemistry (IHC) methods that may be used to visualize tissue-resident macrophages in rats.
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Affiliation(s)
- Stephen Huang
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Emma Maxwell
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Omkar L Patkar
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Katharine M Irvine
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
| | - David A Hume
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
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226
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Chandler RJ, Venditti CP. Gene therapy for organic acidemias: Lessons learned from methylmalonic and propionic acidemia. J Inherit Metab Dis 2024; 47:63-79. [PMID: 37530705 DOI: 10.1002/jimd.12665] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023]
Abstract
Organic acidemias (OA) are a group of rare autosomal recessive disorders of intermediary metabolism that result in a systemic elevation of organic acid. Despite optimal dietary and cofactor therapy, OA patients still suffer from potentially lethal metabolic instability and experience long-term multisystemic complications. Severely affected patients can benefit from elective liver transplantation, which restores hepatic enzymatic activity, improves metabolic stability, and provides the theoretical basis for the pursuit of gene therapy as a new treatment for patients. Because of the poor outcomes reported in those with OA, especially methylmalonic and propionic acidemia, multiple gene therapy approaches have been explored in relevant animal models. Here, we review the results of gene therapy experiments performed using MMA and PA mouse models to illustrate experimental paradigms that could be applicable for all forms of OA.
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Affiliation(s)
- Randy J Chandler
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles P Venditti
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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227
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Tong B, Sun Y. Activation of Young LINE-1 Elements by CRISPRa. Int J Mol Sci 2023; 25:424. [PMID: 38203595 PMCID: PMC10778729 DOI: 10.3390/ijms25010424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long interspersed element-1 (LINE-1; L1s) are mobile genetic elements that comprise nearly 20% of the human genome. L1s have been shown to have important functions in various biological processes, and their dysfunction is thought to be linked with diseases and cancers. However, the roles of the repetitive elements are largely not understood. While the CRISPR activation (CRISPRa) system based on catalytically deadCas9 (dCas9) is widely used for genome-wide interrogation of gene function and genetic interaction, few studies have been conducted on L1s. Here, we report using the CRISPRa method to efficiently activate L1s in human L02 cells, a derivative of the HeLa cancer cell line. After CRISPRa, the young L1 subfamilies such as L1HS/L1PA1 and L1PA2 are found to be expressed at higher levels than the older L1s. The L1s with high levels of transcription are closer to full-length and are more densely occupied by the YY1 transcription factor. The activated L1s can either be mis-spliced to form chimeric transcripts or act as alternative promoters or enhancers to facilitate the expression of neighboring genes. The method described here can be used for studying the functional roles of young L1s in cultured cells of interest.
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Affiliation(s)
- Bei Tong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhua Sun
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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228
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He Y, Shao S, Chen J. High-Fidelity Identification of Single Nucleotide Polymorphism by Type V CRISPR Systems. ACS Sens 2023; 8:4478-4483. [PMID: 38010835 DOI: 10.1021/acssensors.3c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Accurate and sensitive detection of single nucleotide polymorphism (SNP) holds significant clinical implications, especially in the field of cancer diagnosis. Leveraging its high accuracy and programmability, the CRISPR system emerges as a promising platform for advancing the identification of SNPs. In this study, we compared two type V CRISPR/Cas systems (Cas12a and Cas14a) for the identification of cancer-related SNP. Their identification performances were evaluated by characterizing their mismatch tolerance to the BRAF gene. We found that the CRISPR/Cas14a system exhibited superior accuracy and robustness over the CRISPR/Cas12a system for SNP detection. Furthermore, blocker displacement amplification (BDA) was combined with the CRISPR/Cas14a system to eliminate the interference of the wild type (WT) and increase the detection accuracy. In this strategy, we were able to detect BRAF V600E as low as 103 copies with a sensitivity of 0.1% variant allele frequency. Moreover, the BDA-assisted CRISPR/Cas14a system has been applied to identify the BRAF mutation from human colorectal carcinoma cells, achieving a high sensitivity of 0.5% variant allele frequency, which is comparable to or even superior to those of most commercially available products. This work has broadened the scope of the CRISPR system and provided a promising method for precision medicine.
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Affiliation(s)
- Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shengjie Shao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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229
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Li H, Przybyla L, Blanchard JW. Editorial: Understanding human biology with iPSC derived cell types in the Era of CRISPR technology. Front Cell Dev Biol 2023; 11:1351676. [PMID: 38188018 PMCID: PMC10767646 DOI: 10.3389/fcell.2023.1351676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/09/2024] Open
Affiliation(s)
- Huinan Li
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA, United States
| | - Joel W. Blanchard
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
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230
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Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE. Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Cell 2023; 186:5840-5858.e36. [PMID: 38134876 PMCID: PMC10794044 DOI: 10.1016/j.cell.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.
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Affiliation(s)
- Thomas Malachowski
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Keerthivasan Raanin Chandradoss
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi Boya
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Linda Zhou
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashley L Cook
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chuanbin Su
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Pham
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Spencer A Haws
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ji Hun Kim
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Han-Seul Ryu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chunmin Ge
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer M Luppino
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Son C Nguyen
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Katelyn R Titus
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Wanfeng Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Owen Wallace
- Fulcrum Therapeutics Incorporated, Cambridge, MA, USA
| | - Eric F Joyce
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Fulcrum Therapeutics Incorporated, Cambridge, MA, USA
| | | | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
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231
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Parra-Rivas LA, Madhivanan K, Aulston BD, Wang L, Prakashchand DD, Boyer NP, Saia-Cereda VM, Branes-Guerrero K, Pizzo DP, Bagchi P, Sundar VS, Tang Y, Das U, Scott DA, Rangamani P, Ogawa Y, Subhojit Roy. Serine-129 phosphorylation of α-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function. Neuron 2023; 111:4006-4023.e10. [PMID: 38128479 PMCID: PMC10766085 DOI: 10.1016/j.neuron.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/08/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023]
Abstract
Phosphorylation of α-synuclein at the serine-129 site (α-syn Ser129P) is an established pathologic hallmark of synucleinopathies and a therapeutic target. In physiologic states, only a fraction of α-syn is phosphorylated at this site, and most studies have focused on the pathologic roles of this post-translational modification. We found that unlike wild-type (WT) α-syn, which is widely expressed throughout the brain, the overall pattern of α-syn Ser129P is restricted, suggesting intrinsic regulation. Surprisingly, preventing Ser129P blocked activity-dependent synaptic attenuation by α-syn-thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments Ser129P, which is a trigger for protein-protein interactions that are necessary for mediating α-syn function at the synapse. AlphaFold2-driven modeling and membrane-binding simulations suggest a scenario where Ser129P induces conformational changes that facilitate interactions with binding partners. Our experiments offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug development.
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Affiliation(s)
- Leonardo A Parra-Rivas
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Kayalvizhi Madhivanan
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Brent D Aulston
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Lina Wang
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Dube Dheeraj Prakashchand
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas P Boyer
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Veronica M Saia-Cereda
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Kristen Branes-Guerrero
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Donald P Pizzo
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, USA
| | - V S Sundar
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Yong Tang
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Utpal Das
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - David A Scott
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yuki Ogawa
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
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232
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Liu Y, Liu W, Wang B. Engineering CRISPR guide RNAs for programmable RNA sensors. Biochem Soc Trans 2023; 51:2061-2070. [PMID: 37955062 PMCID: PMC10754282 DOI: 10.1042/bst20221486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
As the most valuable feature of the CRISPR system, the programmability based on Watson-Crick base pairing has been widely exploited in engineering RNA sensors. The base pairing in these systems offers a connection between the RNA of interest and the CRISPR effector, providing a highly specific mechanism for RNA detection both in vivo and in vitro. In the last decade, despite the many successful RNA sensing approaches developed during the era of CRISPR explosion, a deeper understanding of the characteristics of CRISPR systems and the continuous expansion of the CRISPR family members indicates that the CRISPR-based RNA sensor remains a promising area from which a variety of new functions and applications can be engineered. Here, we present a systematic overview of the various strategies of engineering CRISPR gRNA for programmable RNA detection with an aim to clarify the role of gRNA's programmability among the present limitations and future development of CRISPR-enabled RNA sensors.
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Affiliation(s)
- Yang Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Wei Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou 311100, China
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233
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Joehnk B, Ali N, Voorhies M, Walcott K, Sil A. Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma. mSphere 2023; 8:e0037023. [PMID: 37819140 PMCID: PMC10732100 DOI: 10.1128/msphere.00370-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/17/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Histoplasma is a primary fungal pathogen with the ability to infect otherwise healthy mammalian hosts, causing systemic and sometimes life-threatening disease. Thus far, molecular genetic manipulation of this organism has utilized RNA interference, random insertional mutagenesis, and a homologous recombination protocol that is highly variable and often inefficient. Targeted gene manipulations have been challenging due to poor rates of homologous recombination events in Histoplasma. Interrogation of the virulence strategies of this organism would be highly accelerated by a means of efficiently generating targeted mutations. We have developed a recyclable CRISPR/Cas9 system that can be used to introduce gene disruptions in Histoplasma with high efficiency, thereby allowing disruption of multiple genes.
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Affiliation(s)
- Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Nebat Ali
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, USA
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234
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Ramos PD, Almeida MS, Olsson IAS. What do people think about genetic engineering? A systematic review of questionnaire surveys before and after the introduction of CRISPR. Front Genome Ed 2023; 5:1284547. [PMID: 38192431 PMCID: PMC10773783 DOI: 10.3389/fgeed.2023.1284547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024] Open
Abstract
The advent of CRISPR-Cas9 in 2012 started revolutionizing the field of genetics by broadening the access to a method for precise modification of the human genome. It also brought renewed attention to the ethical issues of genetic modification and the societal acceptance of technology for this purpose. So far, many surveys assessing public attitudes toward genetic modification have been conducted worldwide. Here, we present the results of a systematic review of primary publications of surveys addressing public attitudes toward genetic modification as well as the awareness and knowledge about the technology required for genetic modification. A total of 53 primary publications (1987-2020) focusing on applications in humans and non-human animals were identified, covering countries in four continents. Of the 53 studies, 30 studies from until and including 2012 (pre-CRISPR) address gene therapy in humans and genetic modification of animals for food production and biomedical research. The remaining 23 studies from after 2013 (CRISPR) address gene editing in humans and animals. Across countries, respondents see gene therapy for disease treatment or prevention in humans as desirable and highly acceptable, whereas enhancement is generally met with opposition. When the study distinguishes between somatic and germline applications, somatic gene editing is generally accepted, whereas germline applications are met with ambivalence. The purpose of the application is also important for assessing attitudes toward genetically modified animals: modification in food production is much less accepted than for biomedical application in pre-CRISPR studies. A relationship between knowledge/awareness and attitude toward genetic modification is often present. A critical appraisal of methodology quality in the primary publications with regards to sampling and questionnaire design, development, and administration shows that there is considerable scope for improvement in the reporting of methodological detail. Lack of information is more common in earlier studies, which probably reflects the changing practice in the field.
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Affiliation(s)
- Pedro Dias Ramos
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Strecht Almeida
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ingrid Anna Sofia Olsson
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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235
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Wahbeh MH, Boyd RJ, Yovo C, Rike B, McCallion AS, Avramopoulos D. A Functional Schizophrenia-associated genetic variant near the TSNARE1 and ADGRB1 genes. bioRxiv 2023:2023.12.18.570831. [PMID: 38187620 PMCID: PMC10769312 DOI: 10.1101/2023.12.18.570831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent collaborative genome wide association studies (GWAS) have identified >200 independent loci contributing to risk for schizophrenia (SCZ). The genes closest to these loci have diverse functions, supporting the potential involvement of multiple relevant biological processes; yet there is no direct evidence that individual variants are functional or directly linked to specific genes. Nevertheless, overlap with certain epigenetic marks suggest that most GWAS-implicated variants are regulatory. Based on the strength of association with SCZ and the presence of regulatory epigenetic marks, we chose one such variant near TSNARE1 and ADGRB1, rs4129585, to test for functional potential and assay differences that may drive the pathogenicity of the risk allele. We observed that the variant-containing sequence drives reporter expression in relevant neuronal populations in zebrafish. Next, we introduced each allele into human induced pluripotent cells and differentiated 4 isogenic clones homozygous for the risk allele and 5 clones homozygous for the non-risk allele into neural precursor cells. Employing RNA-seq, we found that the two alleles yield significant transcriptional differences in the expression of 109 genes at FDR <0.05 and 259 genes at FDR <0.1. We demonstrate that these genes are highly interconnected in pathways enriched for synaptic proteins, axon guidance, and regulation of synapse assembly. Exploration of genes near rs4129585 suggests that this variant does not regulate TSNARE1 transcripts, as previously thought, but may regulate the neighboring ADGRB1, a regulator of synaptogenesis. Our results suggest that rs4129585 is a functional common variant that functions in specific pathways likely involved in SCZ risk.
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Affiliation(s)
- Marah H Wahbeh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel J Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Yovo
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bailey Rike
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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236
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Ten Hacken E, Gruber M, Hernández-Sánchez M, Hoffmann GB, Baranowski K, Redd RA, Clement K, Livak K, Wu CJ. Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing. STAR Protoc 2023; 4:102165. [PMID: 37729058 PMCID: PMC10510057 DOI: 10.1016/j.xpro.2023.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/15/2023] [Accepted: 02/16/2023] [Indexed: 09/22/2023] Open
Abstract
Here, we present a protocol to generate B cell restricted mouse models of loss-of-function genetic drivers typical of lymphoproliferative disorders, using stem cell engineering of murine strains carrying B cell restricted Cas9 expression. We describe steps for preparing lentivirus expressing sgRNA-mCherry, isolating hematopoietic stem and progenitor cells, and in vitro transduction. We then detail the transplantation of engineered cells into recipient mice and verification of gene edits. These mouse models represent versatile platforms to model complex disease traits typical of lymphoproliferative disorders. For complete details on the use and execution of this protocol, please refer to ten Hacken et al.,1 ten Hacken et al.,2 and ten Hacken et al.3.
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Affiliation(s)
- Elisa Ten Hacken
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Michaela Gruber
- CEMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Kaitlyn Baranowski
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Robert A Redd
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kenneth Livak
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA; Translational Immunogenomics Laboratory, Dana Farber Cancer Institute, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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237
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Bril O, Schwarzmueller LJ, Moreno LF, Vermeulen L, Léveillé N. Identifying essential long non-coding RNAs in cancer using CRISPRi-based dropout screens. STAR Protoc 2023; 4:102588. [PMID: 37773752 PMCID: PMC10550846 DOI: 10.1016/j.xpro.2023.102588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key regulators in the initiation, growth, and progression of cancer. High-throughput CRISPR-based techniques systematically assess the function of genes or regulatory elements present in the human genome. Here, we present a protocol for identifying essential lncRNAs in cancer using CRISPRi-based dropout screens. We describe steps to select target sites, design guide RNAs, and generate CRISPRi cell lines. We then detail the execution and analysis of CRISPRi-based dropout screens.
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Affiliation(s)
- Oscar Bril
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands
| | - Laura J Schwarzmueller
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands
| | - Leandro F Moreno
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands
| | - Louis Vermeulen
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands
| | - Nicolas Léveillé
- Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands; Oncode Institute, Meibergdreef 9, Amsterdam 1105AZ, The Netherlands.
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238
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Li Z, Reint G, Haapaniemi EM. Protocol for editing fibroblasts with in vitro transcribed Cas9 mRNA and profile off-target editing by optimized GUIDE-seq. STAR Protoc 2023; 4:102662. [PMID: 37889758 PMCID: PMC10641304 DOI: 10.1016/j.xpro.2023.102662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR-Cas9 gene editing is an efficient technique to modify specific sites/regions of DNA. Delivery of the Cas9 by mRNA is particularly promising in pre-clinical genome editing applications for its transient, nonintegrating feature. However, the off-target of Cas9-gRNA still remains a concern and needs a specific monitor. Here, we present a revised protocol to edit fibroblasts by in vitro transcribed Cas9 mRNA and profile its off-target effect by the optimized GUIDE-seq method. This protocol can also be applied to other cell lines. For complete details on the use and execution of this protocol, please refer to Ganna Reint et al. (2021).1.
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Affiliation(s)
- Zhuokun Li
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway.
| | - Ganna Reint
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
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239
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Kainov Y, Zhuravskaya A, Makeyev EV. Protocol for auxin-inducible depletion of the RNA-binding protein PTBP1 in mouse embryonic stem cells. STAR Protoc 2023; 4:102644. [PMID: 37862173 PMCID: PMC10594634 DOI: 10.1016/j.xpro.2023.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Inducible degradation of proteins of interest provides a powerful approach for functional studies. Here, we present a protocol for tightly controlled depletion of the RNA-binding protein PTBP1 in mouse embryonic stem cells (ESCs). We describe steps for establishing an ESC line expressing doxycycline-inducible auxin receptor protein OsTIR1 and tagging endogenous Ptbp1 alleles using CRISPR-Cas9 and homology-directed repair reagents. We then detail procedures for assaying the efficiency of inducible PTBP1 knockdown by immunoblotting. This protocol is adaptable for other protein targets. For complete details on the use and execution of this protocol, please refer to Iannone et al.1.
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Affiliation(s)
- Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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240
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Wang P, Cao Z, Wang Q, Ma X, Wang N, Chen L, Zhao Y, Miao L. Protocol for CRISPR-Cas9-mediated genome editing to study spermatogenesis in Caenorhabditis elegans. STAR Protoc 2023; 4:102720. [PMID: 37967017 PMCID: PMC10684875 DOI: 10.1016/j.xpro.2023.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/03/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023] Open
Abstract
Gene silencing by P-element-induced wimpy testis-interacting RNAs is a mechanism to maintain genome integrity in germ cells. Here, we present a protocol for knockin or knockout editing of male germline genome mediated by CRISPR-Cas9 technology in Caenorhabditis elegans. We describe steps for constructing edited plasmids, microinjecting worms with these plasmids, and screening edited worms. We then detail procedures for dissecting released sperm and their observation with fluorescence microscopy. Engineered worms provide a model for studying hermaphrodite/male fertility or protein localization in vivo. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).1.
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Affiliation(s)
- Peng Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100059, China
| | - Zheng Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiushi Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100059, China
| | - Xiaojing Ma
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100059, China
| | - Ning Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100059, China
| | - Lianwan Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanmei Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Long Miao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100059, China; Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; MOE Key Laboratory of Cell Proliferation and Regulation Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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241
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Sahu S, Sullivan T, Southon E, Caylor D, Geh J, Sharan SK. Protocol for the saturation and multiplexing of genetic variants using CRISPR-Cas9. STAR Protoc 2023; 4:102702. [PMID: 37948185 PMCID: PMC10658368 DOI: 10.1016/j.xpro.2023.102702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Here, we present a multiplexed assay for variant effect protocol to assess the functional impact of all possible genetic variations within a particular genomic region. We describe steps for saturation genome editing by designing and cloning of single-guide RNA (sgRNA). We then detail steps for nucleofection of sgRNA, testing drug response on variants, and amplification of genomic DNA for next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Sahu et al.1.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Dylan Caylor
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Josephine Geh
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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242
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Ravi NS, George A, Mohankumar KM. Protocol for arrayed gRNA screening by base editors in mammalian cell lines using lentiviral system. STAR Protoc 2023; 4:102668. [PMID: 37922314 PMCID: PMC10656259 DOI: 10.1016/j.xpro.2023.102668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/25/2023] [Accepted: 10/04/2023] [Indexed: 11/05/2023] Open
Abstract
Base editing, a CRISPR-based genome engineering technique, enables precise single-nucleotide modifications while minimizing double-strand breaks. Here, we present a protocol for arrayed mutagenesis using base editors to identify regulatory elements within the gamma-globin locus. We describe steps for guide RNA (gRNA) cloning into lentiviral vectors, establishing stable cell lines with base editor expression, transducing gRNAs, and assessing editing efficiency. This protocol can be applied to diverse genomic regions and cell lines for arrayed screening, facilitating genetic research, and target discovery. For complete details on the use and execution of this protocol, please refer to Ravi et al. (2022)1.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India.
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243
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Mojica-Perez SP, Stokes K, Jaklic DC, Jahagirdar S, Uhler M, Parent JM, Niu W. Protocol for selecting single human pluripotent stem cells using a modified micropipetter. STAR Protoc 2023; 4:102629. [PMID: 37804512 PMCID: PMC10565870 DOI: 10.1016/j.xpro.2023.102629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/31/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023] Open
Abstract
Single-cell clonal selection is a critical procedure for generating a homogeneous population of human pluripotent stem cells. Here, we present a protocol that repurposes the STRIPPER Micropipetter, normally used for in vitro fertilization, to pick single stem cells. We describe steps for tool and reagent preparation, single-cell picking, and colony passaging. We then detail procedures for amplification and analysis. Our protocol does not require cell sorting and produces homogenous clonal cultures with more than 50% survival rate. For complete details on the use and execution of this protocol, please refer to Deng et al.1.
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Affiliation(s)
- Sandra P Mojica-Perez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; The Human Stem Cell and Gene Editing Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kyle Stokes
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel C Jaklic
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheetal Jahagirdar
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Uhler
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; The Human Stem Cell and Gene Editing Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jack M Parent
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; The Human Stem Cell and Gene Editing Core, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Wei Niu
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; The Human Stem Cell and Gene Editing Core, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA.
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244
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Wu Y, Sidharta M, Zhong A, Persily B, Li M, Zhou T. Protocol for the design, conduct, and evaluation of prime editing in human pluripotent stem cells. STAR Protoc 2023; 4:102583. [PMID: 37738119 PMCID: PMC10519846 DOI: 10.1016/j.xpro.2023.102583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/25/2023] [Accepted: 08/30/2023] [Indexed: 09/24/2023] Open
Abstract
Prime editing introduces single-nucleotide polymorphism changes, small deletions, or insertions at a specific genome site without double-stranded DNA breaks or the need for the donor template. Here, we present a protocol to design, conduct, and evaluate prime editing in human pluripotent stem cells. We describe steps for pegRNA and nicking sgRNA design and cloning, the prime editing tool electroporation, and the efficiency evaluation using Miseq. We elaborate the process of GBA (N370S) mutation induction and correction as an example. For complete details on the use and execution of this protocol, please refer to Li et al. (2022).1.
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Affiliation(s)
- Youjun Wu
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
| | - Mega Sidharta
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Aaron Zhong
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Benjamin Persily
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Mu Li
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | - Ting Zhou
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.
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245
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Zhou B, Chen Y, Li L, Liu J, Wang Y, Huang Z, Hu Z, Tian R, Li Z. Purification and functional validation of LtCas12a protein. STAR Protoc 2023; 4:102600. [PMID: 37768827 PMCID: PMC10550837 DOI: 10.1016/j.xpro.2023.102600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/29/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Here, we present a protocol for generating LtCas12a protein recognizing distinct TTNA (N represented A, T, C, G) protospacer adjacent motif sequence. We describe steps for transforming and harvesting bacterial cells and protein purification including nickel affinity chromatography and dialysis. We then detail procedures for verification of LtCas12a with cis- and trans-cleavage activities. For complete details on the use and execution of this protocol, please refer to Chen et al. (2023).1.
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Affiliation(s)
- Bo Zhou
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China; Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China
| | - Ye Chen
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Lifang Li
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jiashuo Liu
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuyan Wang
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zheying Huang
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zheng Hu
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China; Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China.
| | - Rui Tian
- Generulor Company Bio-X Lab, Zhuhai 519000, Guangdong, China.
| | - Zhen Li
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China; Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430062, Hubei, China.
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246
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Yang X, Duan S, Li Z, Wang Z, Kon N, Zhang Z, Gu W. Protocol of CRISPR-Cas9 knockout screens for identifying ferroptosis regulators. STAR Protoc 2023; 4:102762. [PMID: 38048220 PMCID: PMC10730373 DOI: 10.1016/j.xpro.2023.102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/25/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023] Open
Abstract
Ferroptosis, an iron-dependent programmed cell death triggered by excessive lipid peroxidation, has shown promising therapeutic potentials in human diseases. Here, we describe a protocol of a CRISPR-Cas9 loss-of-function screen to identify regulators in response to different inducers of ferroptosis. We emphasize the steps of library amplification, drug treatment, high-throughput sequencing preparation, and bioinformatics analysis using model-based analysis of genome-wide CRISPR-Cas9 knockout (MAGeCK). We also present a method to discover the regulators of ferroptosis and verify the potential targets efficiently. For complete details on use and execution of this protocol, please refer to Yang et al. (2023).1.
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Affiliation(s)
- Xin Yang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiming Li
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhe Wang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ning Kon
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA; Department of Pediatrics, and Department of Genetics and Development, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
| | - Wei Gu
- Institute for Cancer Genetics, and Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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247
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Venkataraman M, Yñigez-Gutierrez A, Infante V, MacIntyre A, Fernandes-Júnior PI, Ané JM, Pfleger B. Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes. ACS Synth Biol 2023; 12:3623-3634. [PMID: 37988619 PMCID: PMC10754042 DOI: 10.1021/acssynbio.3c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. This work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.
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Affiliation(s)
- Maya Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Audrey Yñigez-Gutierrez
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - April MacIntyre
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Valent BioSciences, Libertyville, Illinois 60048, United States
| | - Paulo Ivan Fernandes-Júnior
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Brazilian Agricultural Research Corporation (Embrapa), Tropical Semi-Arid Research Center (Embrapa Semiárido), Petrolina, Pernambuco 56302-970, Brazil
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Brian Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
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248
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Petty NE, Radtke S, Fields E, Humbert O, Llewellyn MJ, Laszlo GS, Zhu H, Jerome KR, Walter RB, Kiem HP. Efficient long-term multilineage engraftment of CD33-edited hematopoietic stem/progenitor cells in nonhuman primates. Mol Ther Methods Clin Dev 2023; 31:101121. [PMID: 37868209 PMCID: PMC10585325 DOI: 10.1016/j.omtm.2023.101121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/23/2023] [Indexed: 10/24/2023]
Abstract
Current immunotherapeutic targets are often shared between neoplastic and normal hematopoietic stem and progenitor cells (HSPCs), leading to unwanted on-target, off-tumor toxicities. Deletion or modification of such targets to protect normal HSPCs is, therefore, of great interest. Although HSPC modifications commonly aim to mimic naturally occurring phenotypes, the long-term persistence and safety of gene-edited cells need to be evaluated. Here, we deleted the V-set domain of CD33, the immune-dominant domain targeted by most anti-CD33 antibodies used to treat CD33-positive malignancies, including acute myeloid leukemia, in the HSPCs of two rhesus macaques, performed autologous transplantation after myeloablative conditioning, and followed the animals for up to 3 years. CD33-edited HSPCs engrafted without any delay in recovery of neutrophils, the primary cell type expressing CD33. No impact on the blood composition, reconstitution of the bone marrow stem cell compartment, or myeloid differentiation potential was observed. Up to 20% long-term gene editing in HSPCs and blood cell lineages was seen with robust loss of CD33 detection on myeloid lineages. In conclusion, deletion of the V-set domain of CD33 on HSPCs, progenitors, and myeloid lineages did not show any adverse effects on their homing and engraftment potential or the differentiation and functionality of myeloid progenitors and lineages.
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Affiliation(s)
- Nicholas E. Petty
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stefan Radtke
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Emily Fields
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Olivier Humbert
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mallory J. Llewellyn
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - George S. Laszlo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Roland B. Walter
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hans-Peter Kiem
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
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Bandyopadhyay A, Köpke M, Moon TS. Editorial: CRISPR-aided bioengineering for value-added product development. Front Bioeng Biotechnol 2023; 11:1340377. [PMID: 38152286 PMCID: PMC10751300 DOI: 10.3389/fbioe.2023.1340377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
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Guo J, Zhu Y, Miao P. Nano-Impact Electrochemical Biosensing Based on a CRISPR-Responsive DNA Hydrogel. Nano Lett 2023; 23:11099-11104. [PMID: 37966867 DOI: 10.1021/acs.nanolett.3c03448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Nano-impact electrochemistry (NIE) enables simple, rapid, and high-throughput biocoupling and biomolecular recognition. However, the low effective collision frequency limits the sensitivity. In this study, we propose a novel NIE sensing strategy amplified by the CRISPR-responsive DNA hydrogel and cascade DNA assembly. By controlling the phase transition of DNA hydrogel and the self-electrolysis of silver nanoparticles, we can obtain significant electrochemical responses. The whole process includes target miRNA-induced strand displacement amplification, catalytic hairpin assembly, and CRISPR/Cas trans-cutting. Thus, ultrahigh sensitivity is promised. This NIE biosensing strategy achieves a limit of detection as low as 4.21 aM for miR-141 and demonstrates a high specificity for practical applications. It may have wide applicability in nucleic acid sensing and shows great potential in disease diagnosis.
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Affiliation(s)
- Jiarong Guo
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yulin Zhu
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Peng Miao
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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