1
|
Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 PMCID: PMC11209408 DOI: 10.3390/vaccines12060636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
Collapse
Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India;
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| |
Collapse
|
2
|
Huang S, Dai R, Zhang Z, Zhang H, Zhang M, Li Z, Zhao K, Xiong W, Cheng S, Wang B, Wan Y. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. Int J Mol Sci 2023; 24:13447. [PMID: 37686249 PMCID: PMC10487896 DOI: 10.3390/ijms241713447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, high programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) of Cas enzymes, the scope of CRISPR/Cas systems has expanded beyond gene editing and they have been utilized in various fields, particularly in live-cell imaging and bioanalysis. In this review, we summarize some fundamental working mechanisms and concepts of the CRISPR/Cas systems, describe the recent advances and design principles of CRISPR/Cas mediated techniques employed in live-cell imaging and bioanalysis, highlight the main applications in the imaging and biosensing of a wide range of molecular targets, and discuss the challenges and prospects of CRISPR/Cas systems in live-cell imaging and biosensing. By illustrating the imaging and bio-sensing processes, we hope this review will guide the best use of the CRISPR/Cas in imaging and quantifying biological and clinical elements and inspire new ideas for better tool design in live-cell imaging and bioanalysis.
Collapse
Affiliation(s)
- Shuo Huang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Rui Dai
- Institute of Oceanography, Hainan University, Haikou 570228, China;
| | - Zhiqi Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Han Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Meng Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Zhangjun Li
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Kangrui Zhao
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Wenjun Xiong
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Siyu Cheng
- College of Art and Design, Hainan University, Haikou 570228, China;
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| |
Collapse
|
3
|
McCarthy M, Dodd WB, Lu X, Pritko DJ, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR. Theory for High-Throughput Genetic Interaction Screening. ACS Synth Biol 2023; 12:2290-2300. [PMID: 37463472 PMCID: PMC10443530 DOI: 10.1021/acssynbio.2c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 07/20/2023]
Abstract
Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
Collapse
Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Daniel J. Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Hugo Sanabria
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, United States
| | - Mark A. Blenner
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29631, United States
| |
Collapse
|
4
|
Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
Collapse
Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
5
|
Maity S, Mukherjee R, Banerjee S. Recent Advances and Therapeutic Strategies Using CRISPR Genome Editing Technique for the Treatment of Cancer. Mol Biotechnol 2023; 65:206-226. [PMID: 35999480 DOI: 10.1007/s12033-022-00550-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/10/2022] [Indexed: 01/18/2023]
Abstract
CRISPR genome editing technique has the potential to target cancer cells in a precise manner. The latest advancements have helped to address one of the prominent concerns about this strategy which is the off-target integrations observed with dsDNA and have resulted in more studies being carried out for potentially safer and more targeted gene therapy, so as to make it available for the clinical trials in order to effectively treat cancer. CRISPR screens offer great potential for the high throughput investigation of the gene functionality in various tumors. It extends its capability to identify the tumor growth essential genes, therapeutic resistant genes, and immunotherapeutic responses. CRISPR screens are mostly performed in in vitro models, but latest advancements focus on developing in vivo models to view cancer progression in animal models. It also allows the detection of factors responsible for tumorigenesis. In CRISPR screens key parameters are optimized in order to meet proficient gene targeting efficiencies. It also detects various molecular effectors required for gene regulation in different cancers, essential pathways which modulate cytotoxicity to immunotherapy in cancer cells, important genes which contribute to cancer cell survival in hypoxic states and modulate cancer long non-coding RNAs. The current review focuses on the recent developments in the therapeutic application of CRISPR technology for cancer therapy. Furthermore, the associated challenges and safety concerns along with the various strategies that can be implemented to overcome these drawbacks has been discussed.
Collapse
Affiliation(s)
- Shreyasi Maity
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India
| | - Rishyani Mukherjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India
| | - Satarupa Banerjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, 632 014, Tamil Nadu, India.
| |
Collapse
|
6
|
Naidoo P, Mkhize-Kwitshana ZL. Clustered Regularly Interspaced Short Palindromic Repeats/ CRISPR associated protein 9-mediated editing of Schistosoma mansoni genes: Identifying genes for immunologically potent drug and vaccine development. Rev Soc Bras Med Trop 2022; 55:e0131. [PMID: 35976333 PMCID: PMC9405935 DOI: 10.1590/0037-8682-0131-2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022] Open
Abstract
Schistosomiasis is a neglected acute and chronic tropical disease caused by intestinal (Schistosoma mansoni and Schistosoma japonicum) and urogenital (Schistosoma haematobium) helminth parasites (blood flukes or digenetic trematodes). It afflicts over 250 million people worldwide, the majority of whom reside in impoverished tropical and subtropical regions in sub-Saharan Africa. Schistosomiasis is the second most common devastating parasitic disease in the world after malaria and causes over 200,000 deaths annually. Currently, there is no effective and approved vaccine available for human use, and treatment strongly relies on praziquantel drug therapy, which is ineffective in killing immature larval schistosomula stages and eggs already lodged in the tissues. The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9 (CRISPR/Cas9)-mediated gene editing tool is used to deactivate a gene of interest to scrutinize its role in health and disease, and to identify genes for vaccine and drug targeting. The present review aims to summarize the major findings from the current literature reporting the usage of CRISPR/Cas9-mediated gene editing to inactivate genes in S. mansoni (acetylcholinesterase (AChE), T2 ribonuclease omega-1 (ω1), sulfotransferase oxamniquine resistance protein (SULT-OR), and α-N-acetylgalactosaminidase (SmNAGAL)), and freshwater gastropod snails, Biomphalaria glabrata (allograft inflammatory factor (BgAIF)), an obligatory component of the life cycle of S. mansoni, to identify their roles in the pathogenesis of schistosomiasis, and to highlight the importance of such studies in identifying and developing drugs and vaccines with high therapeutic efficacy.
Collapse
Affiliation(s)
- Pragalathan Naidoo
- University of KwaZulu-Natal, College of Health Sciences, Department of Medical Microbiology, Durban, KwaZulu-Natal, South Africa.,South African Medical Research Council (SAMRC), Division of Research Capacity Development, Cape Town, Western Cape, South Africa
| | - Zilungile Lynette Mkhize-Kwitshana
- University of KwaZulu-Natal, College of Health Sciences, Department of Medical Microbiology, Durban, KwaZulu-Natal, South Africa.,South African Medical Research Council (SAMRC), Division of Research Capacity Development, Cape Town, Western Cape, South Africa
| |
Collapse
|
7
|
Chupradit K, Thongsin N, Tayapiwatana C, Wattanapanitch M. A precise gene delivery approach for human induced pluripotent stem cells using Cas9 RNP complex and recombinant AAV6 donor vectors. PLoS One 2022; 17:e0270963. [PMID: 35797389 PMCID: PMC9262223 DOI: 10.1371/journal.pone.0270963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Genome editing in human induced pluripotent stem cells (hiPSCs) offers a potential tool for studying gene functions in disease models and correcting genetic mutations for cell-based therapy. Precise transgene insertion in hiPSCs represents a significant challenge. In the past decade, viral transduction has been widely used due to its high transduction efficiency; however, it can result in random transgene integration and variable transgene copy numbers. Non-viral-based strategies are generally safer but limited by their low transfection efficiency in hiPSCs. Recently, genome engineering using adeno-associated virus (AAV) vectors has emerged as a promising gene delivery approach due to AAVs’ low immunogenicity, toxicity, and ability to infect a broad range of cells. The following protocol describes the workflow for genome editing in hiPSCs using the CRISPR/Cas9 ribonucleoprotein (RNP) complex combined with the recombinant AAV serotype 6 (AAV6) donor vectors to introduce a gene of interest (GOI) fused with mCherry fluorescent reporter gene into the AAVS1 safe harbor site. This approach leads to efficient transgene insertion and is applicable to precise genome editing of hiPSCs or other types of stem cells for research purposes.
Collapse
Affiliation(s)
- Koollawat Chupradit
- Research Department, Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Nontaphat Thongsin
- Research Department, Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chatchai Tayapiwatana
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Methichit Wattanapanitch
- Research Department, Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
| |
Collapse
|
8
|
Zhou Y, Fu Q, Shi H, Zhou G. CRISPR Guide RNA Library Screens in Human Induced Pluripotent Stem Cells. Methods Mol Biol 2022; 2549:233-257. [PMID: 35347694 DOI: 10.1007/7651_2021_455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High-throughput CRISPR guide RNA (gRNA) library screen, that is, CRISPR/Cas9 screen, enables the unbiased identification of gene functions in a variety of biological processes. Typical pooled CRISPR/Cas9 screen couples a gRNA library and a guided Cas9 or dCas9 endonuclease to target specific gene loci, and then systematically uncover the causal link between candidate genes and observed cellular phenotypes via gRNA depletion or enrichment in screens. Here, we describe a detailed method of puromycin (PURO) concentration titration and lentiviral CRISPR gRNA library titration in Cas9 expressing monoclonal human iPSC line (Cas9+MNhiPSC) prior to performing the screens, conducting pooled CRISPR gRNA library screens in Cas9+MNhiPSC, genomic DNA extraction from the selected cell subpopulation and sequencing library preparation as well as next generation sequencing (NGS) to generate gRNA read counts. In CRISPR/Cas9 screen, we aim for 30% transduction efficiency (i.e., multiplicity of infection = 0.3) to ensure most of infected cells receive only one gRNA. The principles in this method can be applied to CRISPR perturbation (knockout, activation, repression or base editing) screens with other CRISPR gRNA libraries across many other cell models and other species.
Collapse
Affiliation(s)
- Yan Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Science Center, Shenzhen University, Shenzhen, China.
- Lungene Technologies Co., Ltd, Shenzhen, China.
| | - Qiang Fu
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Huijun Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Xinjiang, China
| | - Guangqian Zhou
- Department of Medical Cell Biology and Genetics, Guangdong Key Laboratory of Genomic Stability and Disease Prevention, Shenzhen Key Laboratory of Anti-aging and Regenerative Medicine, and Shenzhen Engineering Laboratory of Regenerative Technologies for Orthopaedic Diseases, Health Science Center, Shenzhen University, Shenzhen, China
| |
Collapse
|
9
|
Shortt K, Heruth DP. Identification of Genes Regulating Hepatocyte Injury by a Genome-Wide CRISPR-Cas9 Screen. Methods Mol Biol 2022; 2544:227-251. [PMID: 36125723 DOI: 10.1007/978-1-0716-2557-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene editing introduces stable mutations into the genome and has powerful applications extending from research to clinical gene therapy. CRISPR-Cas9 gene editing can be employed to study directly the functional impact of stable gene knockout, activation, and knockdown. Here, we describe the end-to-end methodology by which we employ genome-wide CRISPR-Cas9 knockout to study drug toxicity using acetaminophen (APAP) in a hepatocellular carcinoma liver model as an example. This methodology can be extended to other proliferative cell types and chemical metabolic and toxicity models. By employing a massively parallelized genome-wide knockout model, the genes responsible for cellular toxicity and proliferation may be assayed concurrently. Resultant data are interrogated in the context of existing gene expression data, pathway analysis, drug-gene interactions, and orthogonal confirmatory assays to better understand the metabolic mechanisms.
Collapse
Affiliation(s)
| | - Daniel P Heruth
- Children's Mercy Research Institute, Kansas City, MO, USA.
- Department of Pediatrics, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.
| |
Collapse
|
10
|
Magro G, Calistri A, Parolin C. Targeting and Understanding HIV Latency: The CRISPR System against the Provirus. Pathogens 2021; 10:pathogens10101257. [PMID: 34684206 PMCID: PMC8539363 DOI: 10.3390/pathogens10101257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/16/2022] Open
Abstract
The presence of latently infected cells and reservoirs in HIV-1 infected patients constitutes a significant obstacle to achieve a definitive cure. Despite the efforts dedicated to solve these issues, the mechanisms underlying viral latency are still under study. Thus, on the one hand, new strategies are needed to elucidate which factors are involved in latency establishment and maintenance. On the other hand, innovative therapeutic approaches aimed at eradicating HIV infection are explored. In this context, advances of the versatile CRISPR-Cas gene editing technology are extremely promising, by providing, among other advantages, the possibility to target the HIV-1 genome once integrated into cellular DNA (provirus) and/or host-specific genes involved in virus infection/latency. This system, up to now, has been employed with success in numerous in vitro and in vivo studies, highlighting its increasing significance in the field. In this review, we focus on the progresses made in the use of different CRISPR-Cas strategies to target the HIV-1 provirus, and we then discuss recent advancements in the use of CRISPR screens to elucidate the role of host-specific factors in viral latency.
Collapse
Affiliation(s)
| | - Arianna Calistri
- Correspondence: (A.C.); (C.P.); Tel.: +39-049-827-2341 (A.C.); +39-049-827-2365 (C.P.)
| | - Cristina Parolin
- Correspondence: (A.C.); (C.P.); Tel.: +39-049-827-2341 (A.C.); +39-049-827-2365 (C.P.)
| |
Collapse
|
11
|
Nayarisseri A. Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery. Curr Top Med Chem 2021; 20:1651-1660. [PMID: 32614747 DOI: 10.2174/156802662019200701164759] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.
Collapse
Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| |
Collapse
|
12
|
Paraskevopoulos M, McGuigan AP. Application of CRISPR screens to investigate mammalian cell competition. Brief Funct Genomics 2021; 20:135-147. [PMID: 33782689 DOI: 10.1093/bfgp/elab020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 11/14/2022] Open
Abstract
Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a 'super-competitor' status and outcompete the normal epithelium to establish a precancerous field. To date, many genetic drivers of cell competition have been identified predominately through studies in Drosophila. Especially during the last couple of years, ethylmethanesulfonate-based genetic screens have been instrumental to our understanding of the molecular regulators behind some of the most common competition mechanisms in Drosophila, namely competition due to impaired ribosomal function (or anabolism) and mechanical sensitivity. Despite recent findings in Drosophila and in mammalian models of cell competition, the drivers of mammalian cell competition remain largely elusive. Since the discovery of CRISPR/Cas9, its use in functional genomics has been indispensable to uncover novel cancer vulnerabilities. We envision that CRISPR/Cas9 screens will enable systematic, genome-scale probing of mammalian cell competition to discover novel mutations that not only trigger cell competition but also identify novel molecular components that are essential for the recognition and elimination of less fit cells. In this review, we summarize recent contributions that further our understanding of the molecular mechanisms of cell competition by genetic screening in Drosophila, and provide our perspective on how similar and novel screening strategies made possible by whole-genome CRISPR/Cas9 screening can advance our understanding of mammalian cell competition in the future.
Collapse
|
13
|
Kobaisi F, Fayyad N, Sulpice E, Badran B, Fayyad-Kazan H, Rachidi W, Gidrol X. High-throughput synthetic rescue for exhaustive characterization of suppressor mutations in human genes. Cell Mol Life Sci 2020; 77:4209-4222. [PMID: 32270227 PMCID: PMC7588364 DOI: 10.1007/s00018-020-03519-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Inherited or acquired mutations can lead to pathological outcomes. However, in a process defined as synthetic rescue, phenotypic outcome created by primary mutation is alleviated by suppressor mutations. An exhaustive characterization of these mutations in humans is extremely valuable to better comprehend why patients carrying the same detrimental mutation exhibit different pathological outcomes or different responses to treatment. Here, we first review all known suppressor mutations' mechanisms characterized by genetic screens on model species like yeast or flies. However, human suppressor mutations are scarce, despite some being discovered based on orthologue genes. Because of recent advances in high-throughput screening, developing an inventory of human suppressor mutations for pathological processes seems achievable. In addition, we review several screening methods for suppressor mutations in cultured human cells through knock-out, knock-down or random mutagenesis screens on large scale. We provide examples of studies published over the past years that opened new therapeutic avenues, particularly in oncology.
Collapse
Affiliation(s)
- Farah Kobaisi
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Nour Fayyad
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Eric Sulpice
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
| | - Bassam Badran
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Walid Rachidi
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Xavier Gidrol
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France.
| |
Collapse
|
14
|
Liu Q, He D, Xie L. Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature. PLoS Comput Biol 2019; 15:e1007480. [PMID: 31658261 PMCID: PMC6837542 DOI: 10.1371/journal.pcbi.1007480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/07/2019] [Accepted: 10/08/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is a powerful genome editing technology and has a great potential for in vivo gene therapy. Successful translational application of CRISPR-Cas to biomedicine still faces many safety concerns, including off-target side effect, cell fitness problem after CRISPR-Cas treatment, and on-target genome editing side effect in undesired tissues. To solve these issues, it is needed to design sgRNA with high cell-specific efficacy and specificity. Existing single-guide RNA (sgRNA) design tools mainly depend on a sgRNA sequence and the local information of the targeted genome, thus are not sufficient to account for the difference in the cellular response of the same gene in different cell types. To incorporate cell-specific information into the sgRNA design, we develop novel interpretable machine learning models, which integrate features learned from advanced transformer-based deep neural network with cell-specific gene property derived from biological network and gene expression profile, for the prediction of CRISPR-Cas9 and CRISPR-Cas12a efficacy and specificity. In benchmark studies, our models significantly outperform state-of-the-art algorithms. Furthermore, we find that the network-based gene property is critical for the prediction of cell-specific post-treatment cellular response. Our results suggest that the design of efficient and safe CRISPR-Cas needs to consider cell-specific information of genes. Our findings may bolster developing more accurate predictive models of CRISPR-Cas across a broad spectrum of biological conditions as well as provide new insight into developing efficient and safe CRISPR-based gene therapy.
Collapse
Affiliation(s)
- Qiao Liu
- Department of Computer Science, Hunter College, The City University of New York, New York City, NY, United States of America
| | - Di He
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York City, NY, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York City, NY, United States of America
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York City, NY, United States of America
- Ph.D. Program in Biochemistry and Biology, The Graduate Center, The City University of New York, New York City, NY, United States of America
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York City, NY, United States of America
| |
Collapse
|
15
|
Xiao Q, Chen S, Wang Q, Liu Z, Liu S, Deng H, Hou W, Wu D, Xiong Y, Li J, Guo D. CCR5 editing by Staphylococcus aureus Cas9 in human primary CD4 + T cells and hematopoietic stem/progenitor cells promotes HIV-1 resistance and CD4 + T cell enrichment in humanized mice. Retrovirology 2019; 16:15. [PMID: 31186067 PMCID: PMC6560749 DOI: 10.1186/s12977-019-0477-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The chemokine receptor CCR5, which belongs to the superfamily of G protein-coupled receptors, is the major co-receptor for HIV-1 entry. Individuals with a homozygous CCR5Δ32 mutation have a long lasting and increased resistance to HIV-1 infection. Therefore, CCR5 represents an optimal target for HIV-1/AIDS gene therapy. The CRISPR/Cas9 system has been developed as one of the most efficacious gene editing tools in mammalian cells and the small-sized version from Staphylococcus aureus (SaCas9) has an advantage of easier delivery compared to the most commonly used version from Streptococcus pyogenes Cas9 (SpCas9). RESULTS Here, we demonstrated that CCR5 could be specifically and efficiently edited by CRISPR/SaCas9 together with two sgRNAs, which were identified through a screening of 13 sgRNAs. Disruption of CCR5 expression by lentiviral vector-mediated CRISPR/SaCas9 led to increased resistance against HIV-1 infection in human primary CD4+ T cells. Moreover, humanized mice engrafted with CCR5-disrupted CD4+ T cells showed selective survival and enrichment when challenged with CCR5 (R5)-tropic HIV-1 in comparison to mock-treated CD4+ T cells. We also observed CCR5 could be targeted by CRISPR/SaCas9 in human CD34+ hematopoietic stem/progenitor cells without obvious differentiation deficiencies. CONCLUSIONS This work provides an alternative approach to disrupt human CCR5 by CRISPR/SaCas9 for a potential gene therapy strategy against HIV-1/AIDS.
Collapse
Affiliation(s)
- Qiaoqiao Xiao
- Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Zhongshan Erlu 74, Yuexiu District, Guangzhou, 510080 People’s Republic of China
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Shuliang Chen
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Qiankun Wang
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Zhepeng Liu
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Shuai Liu
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Huan Deng
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Wei Hou
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Dongcheng Wu
- Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Yong Xiong
- Department of Pathology, Zhongnan Hospital, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Jiafu Li
- Department of Pathology, Zhongnan Hospital, Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Deyin Guo
- Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Zhongshan Erlu 74, Yuexiu District, Guangzhou, 510080 People’s Republic of China
| |
Collapse
|
16
|
Bai J, Li K, Tang W, Liang Z, Wang X, Feng W, Zhang S, Ren L, Wu S, Han H, Zhao Y. A high-throughput screen for genes essential for PRRSV infection using a piggyBac-based system. Virology 2019; 531:19-30. [DOI: 10.1016/j.virol.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/02/2019] [Accepted: 03/02/2019] [Indexed: 01/11/2023]
|
17
|
Xiao Q, Guo D, Chen S. Application of CRISPR/Cas9-Based Gene Editing in HIV-1/AIDS Therapy. Front Cell Infect Microbiol 2019; 9:69. [PMID: 30968001 PMCID: PMC6439341 DOI: 10.3389/fcimb.2019.00069] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 01/09/2023] Open
Abstract
Despite the fact that great efforts have been made in the prevention and therapy of HIV-1 infection, HIV-1/AIDS remains a major threat to global human health. Highly active antiretroviral therapy (HAART) can suppress virus replication, but it cannot eradicate latent viral reservoirs in HIV-1/AIDS patients. Recently, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has been engineered as an effective gene-editing technology with the potential to treat HIV-1/AIDS. It can be used to target cellular co-factors or HIV-1 genome to reduce HIV-1 infection and clear the provirus, as well as to induce transcriptional activation of latent virus in latent viral reservoirs for elimination. This versatile gene editing technology has been successfully applied to HIV-1/AIDS prevention and reduction in human cells and animal models. Here, we update the rapid progress of CRISPR/Cas9-based HIV-1/AIDS therapy research in recent years and discuss the limitations and future perspectives of its application.
Collapse
Affiliation(s)
- Qiaoqiao Xiao
- School of Basic Medical Sciences, Institute of Medical Virology, Wuhan University, Wuhan, China.,Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Deyin Guo
- Laboratory of Medical Virology, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shuliang Chen
- School of Basic Medical Sciences, Institute of Medical Virology, Wuhan University, Wuhan, China.,Department of Veterinary Biosciences, Center for Retrovirus Research, Ohio State University, Columbus, OH, United States
| |
Collapse
|
18
|
Shortt K, Heruth DP, Zhang N, Wu W, Singh S, Li DY, Zhang LQ, Wyckoff GJ, Qi LS, Friesen CA, Ye SQ. Identification of Novel Regulatory Genes in APAP Induced Hepatocyte Toxicity by a Genome-Wide CRISPR-Cas9 Screen. Sci Rep 2019; 9:1396. [PMID: 30718897 PMCID: PMC6362041 DOI: 10.1038/s41598-018-37940-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022] Open
Abstract
Acetaminophen (APAP) is a commonly used analgesic responsible for more than half of acute liver failure cases. Identification of previously unknown genetic risk factors would provide mechanistic insights and novel therapeutic targets for APAP-induced liver injury. This study used a genome-wide CRISPR-Cas9 screen to evaluate genes that are protective against, or cause susceptibility to, APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR-Cas9 gene knockouts were treated with 15 mM APAP for 30 minutes to 4 days. A gene expression profile was developed based on the 1) top screening hits, 2) overlap of expression data from APAP overdose studies, and 3) predicted affected biological pathways. We further demonstrated the implementation of intermediate time points for the identification of early and late response genes. This study illustrated the power of a genome-wide CRISPR-Cas9 screen to systematically identify novel genes involved in APAP-induced hepatotoxicity and to provide potential targets to develop novel therapeutic modalities.
Collapse
Affiliation(s)
- Katherine Shortt
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA
- Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
- Division of Cell Biology and Biophysics, University of Missouri Kansas City School of Biological Sciences, Kansas City, MO, USA
- Precision Genomics, Intermountain Healthcare, St. George, UT, 84790, USA
| | - Daniel P Heruth
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA.
| | - NiNi Zhang
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA
- Division of Gastroenterology, Hepatology, Nutrition, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, Tangdu Hospital, The Fourth Military Medical University, Xian, China
| | - Weibin Wu
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA
- Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Shipra Singh
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA
- Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Ding-You Li
- Division of Gastroenterology, Hepatology, Nutrition, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Li Qin Zhang
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA.
- Department of Biomedical Sciences, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.
| | - Gerald J Wyckoff
- Division of Molecular Biology & Biochemistry, University of Missouri Kansas City School of Biological Sciences, Kansas City, MO, USA
| | - Lei S Qi
- Department of Bioengineering, Department of Chemical and Systems Biology, ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Craig A Friesen
- Division of Gastroenterology, Hepatology, Nutrition, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Shui Qing Ye
- Division of Experimental and Translational Genetics, University of Missouri Kansas City School of Medicine, Kansas City, USA
- Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
- Division of Cell Biology and Biophysics, University of Missouri Kansas City School of Biological Sciences, Kansas City, MO, USA
| |
Collapse
|
19
|
Karlgren M, Simoff I, Keiser M, Oswald S, Artursson P. CRISPR-Cas9: A New Addition to the Drug Metabolism and Disposition Tool Box. Drug Metab Dispos 2018; 46:1776-1786. [PMID: 30126863 DOI: 10.1124/dmd.118.082842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9), i.e., CRISPR-Cas9, has been extensively used as a gene-editing technology during recent years. Unlike earlier technologies for gene editing or gene knockdown, such as zinc finger nucleases and RNA interference, CRISPR-Cas9 is comparably easy to use, affordable, and versatile. Recently, CRISPR-Cas9 has been applied in studies of drug absorption, distribution, metabolism, and excretion (ADME) and for ADME model generation. To date, about 50 papers have been published describing in vitro or in vivo CRISPR-Cas9 gene editing of ADME and ADME-related genes. Twenty of these papers describe gene editing of clinically relevant genes, such as ATP-binding cassette drug transporters and cytochrome P450 drug-metabolizing enzymes. With CRISPR-Cas9, the ADME tool box has been substantially expanded. This new technology allows us to develop better and more predictive in vitro and in vivo ADME models and map previously underexplored ADME genes and gene families. In this mini-review, we give an overview of the CRISPR-Cas9 technology and summarize recent applications of CRISPR-Cas9 within the ADME field. We also speculate about future applications of CRISPR-Cas9 in ADME research.
Collapse
Affiliation(s)
- M Karlgren
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - I Simoff
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - M Keiser
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - S Oswald
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| | - P Artursson
- Department of Pharmacy (M.Ka., P.A.), Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Department of Pharmacy (I.S.), and Science for Life Laboratory (P.A.), Uppsala University, Uppsala, Sweden; and Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine of Greifswald, Germany (M.Ke., S.O.)
| |
Collapse
|
20
|
Sun W, He B, Yang B, Hu W, Cheng S, Xiao H, Yang Z, Wen X, Zhou L, Xie H, Shen X, Wu J, Zheng S. Genome-wide CRISPR screen reveals SGOL1 as a druggable target of sorafenib-treated hepatocellular carcinoma. J Transl Med 2018; 98:734-744. [PMID: 29467456 DOI: 10.1038/s41374-018-0027-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/28/2017] [Accepted: 01/06/2018] [Indexed: 02/08/2023] Open
Abstract
The genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen is a powerful tool used to identify therapeutic targets that can be harnessed for cancer treatment. This study aimed to assess the efficacy of genome-wide CRISPR screening to identify druggable genes associated with sorafenib-treated hepatocellular carcinoma (HCC). A genome-scale CRISPR knockout (GeCKO v2) library containing 123,411 single guide RNAs (sgRNAs) was used to identify loss-of-function mutations conferring sorafenib resistance upon HCC cells. Resistance gene screens identified SGOL1 as an indicator of prognosis of patients treated with sorafenib. Of the 19,050 genes tested, the knockout screen identified inhibition of SGOL1 expression as the most-effective genetic suppressor of sorafenib activity. Analysis of the survival of 210 patients with HCC after hepatic resection revealed that high SGOL1 expression shortened overall survival (P = 0.021). Further, matched pairs analysis of the TCGA database revealed that SGOL1 is differentially expressed. When we used a lentivirus Cas9 vector to determine the effect of targeting SGOL1 with a specific sgRNA in HCC cells, we found that SGOL1 expression was efficiently inhibited and that loss of SGOL1 was associated with sorafenib resistance. Further, loss of SGOL1 from HCC cell decreased the cytotoxicity of sorafenib in vivo. We conclude that the CRISPR screen is a powerful tool for therapeutic target analysis of sorafenib treatment and that SGOL1 serves as a druggable target for HCC treated with sorafenib and an indicator of prognosis.
Collapse
Affiliation(s)
- Weijian Sun
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Bin He
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Beng Yang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Wendi Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Shaobing Cheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Heng Xiao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Zhengjie Yang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Xiaoyu Wen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China.,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China
| | - Xian Shen
- Department of Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China. .,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China. .,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China. .,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Zhejiang Province, Hangzhou, 310003, China. .,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou, 310003, China.
| |
Collapse
|
21
|
Lyu C, Shen J, Wang R, Gu H, Zhang J, Xue F, Liu X, Liu W, Fu R, Zhang L, Li H, Zhang X, Cheng T, Yang R, Zhang L. Targeted genome engineering in human induced pluripotent stem cells from patients with hemophilia B using the CRISPR-Cas9 system. Stem Cell Res Ther 2018; 9:92. [PMID: 29625575 PMCID: PMC5889534 DOI: 10.1186/s13287-018-0839-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/22/2018] [Accepted: 03/13/2018] [Indexed: 02/12/2023] Open
Abstract
Background Replacement therapy for hemophilia remains a lifelong treatment. Only gene therapy can cure hemophilia at a fundamental level. The clustered regularly interspaced short palindromic repeats–CRISPR associated nuclease 9 (CRISPR-Cas9) system is a versatile and convenient genome editing tool which can be applied to gene therapy for hemophilia. Methods A patient’s induced pluripotent stem cells (iPSCs) were generated from their peripheral blood mononuclear cells (PBMNCs) using episomal vectors. The AAVS1-Cas9-sgRNA plasmid which targets the AAVS1 locus and the AAVS1-EF1α-F9 cDNA-puromycin donor plasmid were constructed, and they were electroporated into the iPSCs. When insertion of F9 cDNA into the AAVS1 locus was confirmed, whole genome sequencing (WGS) was carried out to detect the off-target issue. The iPSCs were then differentiated into hepatocytes, and human factor IX (hFIX) antigen and activity were measured in the culture supernatant. Finally, the hepatocytes were transplanted into non-obese diabetic/severe combined immunodeficiency disease (NOD/SCID) mice through splenic injection. Results The patient’s iPSCs were generated from PBMNCs. Human full-length F9 cDNA was inserted into the AAVS1 locus of iPSCs of a hemophilia B patient using the CRISPR-Cas9 system. No off-target mutations were detected by WGS. The hepatocytes differentiated from the inserted iPSCs could secrete hFIX stably and had the ability to be transplanted into the NOD/SCID mice in the short term. Conclusions PBMNCs are good somatic cell choices for generating iPSCs from hemophilia patients. The iPSC technique is a good tool for genetic therapy for human hereditary diseases. CRISPR-Cas9 is versatile, convenient, and safe to be used in iPSCs with low off-target effects. Our research offers new approaches for clinical gene therapy for hemophilia. Electronic supplementary material The online version of this article (10.1186/s13287-018-0839-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cuicui Lyu
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.,Department of Hematology, The First Central Hospital of Tianjin, Tianjin, 300192, China
| | - Jun Shen
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Rui Wang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Haihui Gu
- Department of Transfusion Medicine, Shanghai Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Jianping Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Feng Xue
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Xiaofan Liu
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Wei Liu
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Rongfeng Fu
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Liyan Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Huiyuan Li
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Xiaobing Zhang
- Division of Regenerative Medicine MC1528B, Department of Medicine, Loma Linda University, 11234 Anderson Street, Loma Linda, CA, 92350, USA
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Gene Therapy of Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.
| |
Collapse
|
22
|
PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep 2017; 7:15854. [PMID: 29158538 PMCID: PMC5696473 DOI: 10.1038/s41598-017-16193-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/08/2017] [Indexed: 12/26/2022] Open
Abstract
Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets.
Collapse
|
23
|
Dhanjal JK, Radhakrishnan N, Sundar D. Identifying synthetic lethal targets using CRISPR/Cas9 system. Methods 2017; 131:66-73. [PMID: 28710008 DOI: 10.1016/j.ymeth.2017.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 12/26/2022] Open
Abstract
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets. It mainly includes CRISPR library to be used, cell types for conducting the experiment, the most appropriate screening strategy and ways of selecting the desired phenotypes from the complete cell population. The complete knockdown of genes can be achieved using CRISPR/Cas9 knockout libraries. For higher quality loss-of-function screens, haploid cells with defective homology-directed DNA repair mechanism could be used. Two widely used screening formats include arrayed and pooled screens followed by negative or positive selection of the cells with desired phenotype. However, pooled screening format with negative selection of cells serves the best. The advantages of using CRISPR/Cas9 system over the other RNAi approaches have also been discussed. Finally, some studies using CRISPR/Cas9 for genome-wide knockout screening in human cells and computational approaches for identification of synthetic lethal interactions have been discussed.
Collapse
Affiliation(s)
- Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Navaneethan Radhakrishnan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| |
Collapse
|
24
|
Lin J, Zhou Y, Liu J, Chen J, Chen W, Zhao S, Wu Z, Wu N. Progress and Application of CRISPR/Cas Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3061-3071. [DOI: 10.1002/jcb.26198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Internal Medicine, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Department of Breast Surgical Oncology, National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Central Laboratory, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| |
Collapse
|
25
|
Crauciuc A, Tripon F, Gheorghiu A, Nemes G, Boglis A, Banescu C. Review. Development, Applications, Benefits, Challenges and Limitations of the New Genome Engineering Technique. An Update Study. ACTA MEDICA MARISIENSIS 2017. [DOI: 10.1515/amma-2017-0007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
We assume that the CRISPR Cas9 theory must be delimited by applicability, because the consequences of long term DNA manipulation remain unknown. Moreover, the irreversibility of this procedure should instigate researchers to reserved opinions.
Usefulness as well as benefits of CRISPR Cas9 made it one of the most popular and used genome editing technique. But with its huge potential, ethical and safety concerns emerge. Therefore, before continuing research in this direction we should have a well organized system that is able to make that differentiation between research and reproduction. However we truly believe in the future of genetic engineering and with the CRISPR-Cas9 system we expect that the opportunity of treating now so called incurable diseases arises. Time is all we need.
Collapse
Affiliation(s)
| | - Florin Tripon
- University of Medicine and Pharmacy Tirgu Mures, Romania
| | | | | | - Alina Boglis
- University of Medicine and Pharmacy Tirgu Mures, Romania
| | - Claudia Banescu
- University of Medicine and Pharmacy Tirgu Mures, Romania Romania
- Center for Advanced Medical and Pharmaceutical Research, University of Medicine and Pharmacy Tirgu Mureș, Romania
| |
Collapse
|
26
|
Thompson N, Adams DJ, Ranzani M. Synthetic lethality: emerging targets and opportunities in melanoma. Pigment Cell Melanoma Res 2017; 30:183-193. [PMID: 28097822 PMCID: PMC5396340 DOI: 10.1111/pcmr.12573] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/11/2017] [Indexed: 02/06/2023]
Abstract
Great progress has been made in the treatment of melanoma through use of targeted therapies and immunotherapy. One approach that has not been fully explored is synthetic lethality, which exploits somatically acquired changes, usually driver mutations, to specifically kill tumour cells. We outline the various approaches that may be applied to identify synthetic lethal interactions and define how these interactions may drive drug discovery efforts.
Collapse
Affiliation(s)
- Nicola Thompson
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Marco Ranzani
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| |
Collapse
|
27
|
Lu XJ, Sun HM, Xu Y, Yu X, Gu B. The applications and advances of CRISPR-Cas9 in medical research. Brief Funct Genomics 2017; 16:1-3. [PMID: 28132023 DOI: 10.1093/bfgp/elw036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiao-Jie Lu
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Mei Sun
- Department of Anesthesiology, Jiangsu Huai'an Maternity and Children Hospital, Huai'an, China
| | - Yong Xu
- Department of Nephrology,, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Xi Yu
- Department of Gastroenterology, Longgang District Central Hospital of Shenzhen, Longgang District, Shenzhen, Guangdong, China
| | - Biao Gu
- Department of Thoracic Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| |
Collapse
|
28
|
The Role of Noncoding RNAs in Neurodevelopmental Disorders: The Case of Rett Syndrome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:23-37. [DOI: 10.1007/978-3-319-53889-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
29
|
Pasipoularides A. Genomic translational research: Paving the way to individualized cardiac functional analyses and personalized cardiology. Int J Cardiol 2016; 230:384-401. [PMID: 28057368 DOI: 10.1016/j.ijcard.2016.12.097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/27/2016] [Accepted: 12/17/2016] [Indexed: 01/08/2023]
Abstract
For most of Medicine's past, the best that physicians could do to cope with disease prevention and treatment was based on the expected response of an average patient. Currently, however, a more personalized/precise approach to cardiology and medicine in general is becoming possible, as the cost of sequencing a human genome has declined substantially. As a result, we are witnessing an era of precipitous advances in biomedicine and bourgeoning understanding of the genetic basis of cardiovascular and other diseases, reminiscent of the resurgence of innovations in physico-mathematical sciences and biology-anatomy-cardiology in the Renaissance, a parallel time of radical change and reformation of medical knowledge, education and practice. Now on the horizon is an individualized, diverse patient-centered, approach to medical practice that encompasses the development of new, gene-based diagnostics and preventive medicine tactics, and offers the broadest range of personalized therapies based on pharmacogenetics. Over time, translation of genomic and high-tech approaches unquestionably will transform clinical practice in cardiology and medicine as a whole, with the adoption of new personalized medicine approaches and procedures. Clearly, future prospects far outweigh present accomplishments, which are best viewed as a promising start. It is now essential for pluridisciplinary health care providers to examine the drivers and barriers to the clinical adoption of this emerging revolutionary paradigm, in order to expedite the realization of its potential. So, we are not there yet, but we are definitely on our way.
Collapse
Affiliation(s)
- Ares Pasipoularides
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA.
| |
Collapse
|
30
|
Doerflinger M, Forsyth W, Ebert G, Pellegrini M, Herold MJ. CRISPR/Cas9-The ultimate weapon to battle infectious diseases? Cell Microbiol 2016; 19. [PMID: 27860197 DOI: 10.1111/cmi.12693] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/30/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022]
Abstract
Infectious diseases are a leading cause of death worldwide. Novel therapeutics are urgently required to treat multidrug-resistant organisms such as Mycobacterium tuberculosis and to mitigate morbidity and mortality caused by acute infections such as malaria and dengue fever virus as well as chronic infections such as human immunodeficiency virus-1 and hepatitis B virus. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, which has revolutionized biomedical research, holds great promise for the identification and validation of novel drug targets. Since its discovery as an adaptive immune system in prokaryotes, the CRISPR/Cas9 system has been developed into a multi-faceted genetic modification tool, which can now be used to induce gene deletions or specific gene insertions, such as conditional alleles or endogenous reporters in virtually any organism. The generation of CRISPR/Cas9 libraries that can be used to perform phenotypic whole genome screens provides an important new tool that will aid in the identification of critical host factors involved in the pathogenesis of infectious diseases. In this review, we will discuss the development and recent applications of the CRISPR/Cas9 system used to identify novel regulators, which might become important in the fight against infectious diseases.
Collapse
Affiliation(s)
- M Doerflinger
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - W Forsyth
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - G Ebert
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M Pellegrini
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
31
|
Leung AWY, de Silva T, Bally MB, Lockwood WW. Synthetic lethality in lung cancer and translation to clinical therapies. Mol Cancer 2016; 15:61. [PMID: 27686855 PMCID: PMC5041331 DOI: 10.1186/s12943-016-0546-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/21/2016] [Indexed: 01/06/2023] Open
Abstract
Lung cancer is a heterogeneous disease consisting of multiple histological subtypes each driven by unique genetic alterations. Despite the development of targeted therapies that inhibit the oncogenic mutations driving a subset of lung cancer cases, there is a paucity of effective treatments for the majority of lung cancer patients and new strategies are urgently needed. In recent years, the concept of synthetic lethality has been established as an effective approach for discovering novel cancer-specific targets as well as a method to improve the efficacy of existing drugs which provide partial but insufficient benefits for patients. In this review, we discuss the concept of synthetic lethality, the various types of synthetic lethal interactions in the context of oncology and the approaches used to identify these interactions, including recent advances that have transformed the ability to discover novel synthetic lethal combinations on a global scale. Lastly, we describe the specific synthetic lethal interactions identified in lung cancer to date and explore the pharmacological challenges and considerations in translating these discoveries to the clinic.
Collapse
Affiliation(s)
- Ada W. Y. Leung
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
| | - Tanya de Silva
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
| | - Marcel B. Bally
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
- Centre for Drug Research and Development, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
| | - William W. Lockwood
- Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227-2211 Wesbrook Mall, Vancouver, BC V6T 2B5 Canada
- Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC V5Z 1L3 Canada
| |
Collapse
|
32
|
Precision Medicine and Advancing Genetic Technologies—Disability and Human Rights Perspectives. LAWS 2016. [DOI: 10.3390/laws5030036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
33
|
A genome editing primer for the hematologist. Blood 2016; 127:2525-35. [PMID: 27053532 DOI: 10.1182/blood-2016-01-678151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Gene editing enables the site-specific modification of the genome. These technologies have rapidly advanced such that they have entered common use in experimental hematology to investigate genetic function. In addition, genome editing is becoming increasingly plausible as a treatment modality to rectify genetic blood disorders and improve cellular therapies. Genome modification typically ensues from site-specific double-strand breaks and may result in a myriad of outcomes. Even single-strand nicks and targeted biochemical modifications that do not permanently alter the DNA sequence (epigenome editing) may be powerful instruments. In this review, we examine the various technologies, describe their advantages and shortcomings for engendering useful genetic alterations, and consider future prospects for genome editing to impact hematology.
Collapse
|
34
|
Zhang JH, Adikaram P, Pandey M, Genis A, Simonds WF. Optimization of genome editing through CRISPR-Cas9 engineering. Bioengineered 2016; 7:166-74. [PMID: 27340770 PMCID: PMC4927198 DOI: 10.1080/21655979.2016.1189039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats)-Cas9 (CRISPR associated protein 9) has rapidly become the most promising genome editing tool with great potential to revolutionize medicine. Through guidance of a 20 nucleotide RNA (gRNA), CRISPR-Cas9 finds and cuts target protospacer DNA precisely 3 base pairs upstream of a PAM (Protospacer Adjacent Motif). The broken DNA ends are repaired by either NHEJ (Non-Homologous End Joining) resulting in small indels, or by HDR (Homology Directed Repair) for precise gene or nucleotide replacement. Theoretically, CRISPR-Cas9 could be used to modify any genomic sequences, thereby providing a simple, easy, and cost effective means of genome wide gene editing. However, the off-target activity of CRISPR-Cas9 that cuts DNA sites with imperfect matches with gRNA have been of significant concern because clinical applications require 100% accuracy. Additionally, CRISPR-Cas9 has unpredictable efficiency among different DNA target sites and the PAM requirements greatly restrict its genome editing frequency. A large number of efforts have been made to address these impeding issues, but much more is needed to fully realize the medical potential of CRISPR-Cas9. In this article, we summarize the existing problems and current advances of the CRISPR-Cas9 technology and provide perspectives for the ultimate perfection of Cas9-mediated genome editing.
Collapse
Affiliation(s)
- Jian-Hua Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Poorni Adikaram
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mritunjay Pandey
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Allison Genis
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - William F. Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
35
|
CRISPR-Cas9 for in vivo Gene Therapy: Promise and Hurdles. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e349. [PMID: 28131272 PMCID: PMC5023403 DOI: 10.1038/mtna.2016.58] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/19/2016] [Indexed: 12/18/2022]
Abstract
Owing to its easy-to-use and multiplexing nature, the genome editing tool CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats (CRISPR) associated nuclease 9) is revolutionizing many areas of medical research and one of the most amazing areas is its gene therapy potentials. Previous explorations into the therapeutic potentials of CRISPR-Cas9 were mainly conducted in vitro or in animal germlines, the translatability of which, however, is either limited (to tissues with adult stem cells amenable to culture and manipulation) or currently impermissible (due to ethic concerns). Recently, important progresses have been made on this regard. Several studies have demonstrated the ability of CRISPR-Cas9 for in vivo gene therapy in adult rodent models of human genetic diseases delivered by methods that are potentially translatable to human use. Although these recent advances represent a significant step forward to the eventual application of CRISPR-Cas9 to the clinic, there are still many hurdles to overcome, such as the off-target effects of CRISPR-Cas9, efficacy of homology-directed repair, fitness of edited cells, immunogenicity of therapeutic CRISPR-Cas9 components, as well as efficiency, specificity, and translatability of in vivo delivery methods. In this article, we introduce the mechanisms and merits of CRISPR-Cas9 in genome editing, briefly retrospect the applications of CRISPR-Cas9 in gene therapy explorations and highlight recent advances, later we discuss in detail the challenges lying ahead in the way of its translatability, propose possible solutions, and future research directions.
Collapse
|