1
|
Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
Collapse
Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| |
Collapse
|
2
|
Kim HS, Kweon J, Kim Y. Recent advances in CRISPR-based functional genomics for the study of disease-associated genetic variants. Exp Mol Med 2024; 56:861-869. [PMID: 38556550 PMCID: PMC11058232 DOI: 10.1038/s12276-024-01212-3] [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: 07/31/2023] [Revised: 01/15/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Advances in sequencing technology have greatly increased our ability to gather genomic data, yet understanding the impact of genetic mutations, particularly variants of uncertain significance (VUSs), remains a challenge in precision medicine. The CRISPR‒Cas system has emerged as a pivotal tool for genome engineering, enabling the precise incorporation of specific genetic variations, including VUSs, into DNA to facilitate their functional characterization. Additionally, the integration of CRISPR‒Cas technology with sequencing tools allows the high-throughput evaluation of mutations, transforming uncertain genetic data into actionable insights. This allows researchers to comprehensively study the functional consequences of point mutations, paving the way for enhanced understanding and increasing application to precision medicine. This review summarizes the current genome editing tools utilizing CRISPR‒Cas systems and their combination with sequencing tools for functional genomics, with a focus on point mutations.
Collapse
Affiliation(s)
- Heon Seok Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seongdong-gu, Seoul, Republic of Korea
| | - Jiyeon Kweon
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
3
|
Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
Collapse
Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
4
|
Fu Y, He X, Gao XD, Li F, Ge S, Yang Z, Fan X. Prime editing: current advances and therapeutic opportunities in human diseases. Sci Bull (Beijing) 2023; 68:3278-3291. [PMID: 37973465 DOI: 10.1016/j.scib.2023.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/06/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023]
Abstract
Gene editing ushers in a new era of disease treatment since many genetic diseases are caused by base-pair mutations in genomic DNA. With the rapid development of genome editing technology, novel editing tools such as base editing and prime editing (PE) have attracted public attention, heralding a great leap forward in this field. PE, in particular, is characterized by no need for double-strand breaks (DSBs) or homology sequence templates with variable application scenarios, including point mutations as well as insertions or deletions. With higher editing efficiency and fewer byproducts than traditional editing tools, PE holds great promise as a therapeutic strategy for human diseases. Subsequently, a growing demand for the standard construction of PE system has spawned numerous easy-to-access internet resources and tools for personalized prime editing guide RNA (pegRNA) design and off-target site prediction. In this review, we mainly introduce the innovation and evolutionary strategy of PE systems and the auxiliary tools for PE design and analysis. Additionally, its application and future potential in the clinical field have been summarized and envisaged.
Collapse
Affiliation(s)
- Yidian Fu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xiaoyu He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge MA 02138, USA
| | - Fang Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Zhi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200011, China.
| |
Collapse
|
5
|
Xu Z, Ma D, Su H, Jia X, Li Y, Lu Y, Xie Z. Explore the dominant factor in prime editing via a view of DNA processing. Synth Syst Biotechnol 2023; 8:371-377. [PMID: 37325180 PMCID: PMC10265487 DOI: 10.1016/j.synbio.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Prime editing is a revolutionary gene-editing method that is capable of introducing insertions, deletions and base substitutions into the genome. However, the editing efficiency of Prime Editor (PE) is limited by the DNA repair process. Here, we show that overexpression of the flap structure-specific endonuclease 1 (FEN1) and the DNA ligase 1 (LIG1) increases the efficiency of prime editing, which is similar to the dominant negative mutL homolog 1 (MLH1dn). In addition, MLH1 is still the dominant factor over FEN1 and LIG1 in prime editing. Our results help to further understand the relationship of proteins involved in prime editing and envisage future directions for the development of PE.
Collapse
Affiliation(s)
- Zhimeng Xu
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Dacheng Ma
- Research Center for Biological Computation, Zhejiang Laboratory, Hangzhou, 311100, China
| | - Houzhen Su
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Xiaodong Jia
- Comprehensive Liver Cancer Centre, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yinqing Li
- School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Yinying Lu
- Comprehensive Liver Cancer Centre, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
6
|
Doman JL, Pandey S, Neugebauer ME, An M, Davis JR, Randolph PB, McElroy A, Gao XD, Raguram A, Richter MF, Everette KA, Banskota S, Tian K, Tao YA, Tolar J, Osborn MJ, Liu DR. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 2023; 186:3983-4002.e26. [PMID: 37657419 PMCID: PMC10482982 DOI: 10.1016/j.cell.2023.07.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/07/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023]
Abstract
Prime editing enables a wide variety of precise genome edits in living cells. Here we use protein evolution and engineering to generate prime editors with reduced size and improved efficiency. Using phage-assisted evolution, we improved editing efficiencies of compact reverse transcriptases by up to 22-fold and generated prime editors that are 516-810 base pairs smaller than the current-generation editor PEmax. We discovered that different reverse transcriptases specialize in different types of edits and used this insight to generate reverse transcriptases that outperform PEmax and PEmaxΔRNaseH, the truncated editor used in dual-AAV delivery systems. Finally, we generated Cas9 domains that improve prime editing. These resulting editors (PE6a-g) enhance therapeutically relevant editing in patient-derived fibroblasts and primary human T-cells. PE6 variants also enable longer insertions to be installed in vivo following dual-AAV delivery, achieving 40% loxP insertion in the cortex of the murine brain, a 24-fold improvement compared to previous state-of-the-art prime editors.
Collapse
Affiliation(s)
- Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Monica E Neugebauer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kelcee A Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kathryn Tian
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Y Allen Tao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
7
|
Zhang Z, Bao X, Lin CP. Progress and Prospects of Gene Editing in Pluripotent Stem Cells. Biomedicines 2023; 11:2168. [PMID: 37626665 PMCID: PMC10452926 DOI: 10.3390/biomedicines11082168] [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: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
Applying programmable nucleases in gene editing has greatly shaped current research in basic biology and clinical translation. Gene editing in human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), is highly relevant to clinical cell therapy and thus should be examined with particular caution. First, since all mutations in PSCs will be carried to all their progenies, off-target edits of editors will be amplified. Second, due to the hypersensitivity of PSCs to DNA damage, double-strand breaks (DSBs) made by gene editing could lead to low editing efficiency and the enrichment of cell populations with defective genomic safeguards. In this regard, DSB-independent gene editing tools, such as base editors and prime editors, are favored due to their nature to avoid these consequences. With more understanding of the microbial world, new systems, such as Cas-related nucleases, transposons, and recombinases, are also expanding the toolbox for gene editing. In this review, we discuss current applications of programmable nucleases in PSCs for gene editing, the efforts researchers have made to optimize these systems, as well as new tools that can be potentially employed for differentiation modeling and therapeutic applications.
Collapse
Affiliation(s)
| | | | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (Z.Z.); (X.B.)
| |
Collapse
|
8
|
Choi EH, Suh S, Sears AE, Hołubowicz R, Kedhar SR, Browne AW, Palczewski K. Genome editing in the treatment of ocular diseases. Exp Mol Med 2023; 55:1678-1690. [PMID: 37524870 PMCID: PMC10474087 DOI: 10.1038/s12276-023-01057-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/14/2023] [Indexed: 08/02/2023] Open
Abstract
Genome-editing technologies have ushered in a new era in gene therapy, providing novel therapeutic strategies for a wide range of diseases, including both genetic and nongenetic ocular diseases. These technologies offer new hope for patients suffering from previously untreatable conditions. The unique anatomical and physiological features of the eye, including its immune-privileged status, size, and compartmentalized structure, provide an optimal environment for the application of these cutting-edge technologies. Moreover, the development of various delivery methods has facilitated the efficient and targeted administration of genome engineering tools designed to correct specific ocular tissues. Additionally, advancements in noninvasive ocular imaging techniques and electroretinography have enabled real-time monitoring of therapeutic efficacy and safety. Herein, we discuss the discovery and development of genome-editing technologies, their application to ocular diseases from the anterior segment to the posterior segment, current limitations encountered in translating these technologies into clinical practice, and ongoing research endeavors aimed at overcoming these challenges.
Collapse
Affiliation(s)
- Elliot H Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Avery E Sears
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Rafał Hołubowicz
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Sanjay R Kedhar
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Andrew W Browne
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, USA.
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| |
Collapse
|
9
|
Zhao Z, Shang P, Mohanraju P, Geijsen N. Prime editing: advances and therapeutic applications. Trends Biotechnol 2023; 41:1000-1012. [PMID: 37002157 DOI: 10.1016/j.tibtech.2023.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 04/01/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas)-mediated genome editing has revolutionized biomedical research and will likely change the therapeutic and diagnostic landscape. However, CRISPR-Cas9, which edits DNA by activating DNA double-strand break (DSB) repair pathways, is not always sufficient for gene therapy applications where precise mutation repair is required. Prime editing, the latest revolution in genome-editing technologies, can achieve any possible base substitution, insertion, or deletion without the requirement for DSBs. However, prime editing is still in its infancy, and further development is needed to improve editing efficiency and delivery strategies for therapeutic applications. We summarize latest developments in the optimization of prime editor (PE) variants with improved editing efficiency and precision. Moreover, we highlight some potential therapeutic applications.
Collapse
Affiliation(s)
- Zhihan Zhao
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Peng Shang
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Prarthana Mohanraju
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| | - Niels Geijsen
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| |
Collapse
|
10
|
Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
Collapse
Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
11
|
Wolff JH, Mikkelsen JG. Prime editing in hematopoietic stem cells—From ex vivo to in vivo CRISPR-based treatment of blood disorders. Front Genome Ed 2023; 5:1148650. [PMID: 36969373 PMCID: PMC10036844 DOI: 10.3389/fgeed.2023.1148650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Prime editing of human hematopoietic stem cells has the potential to become a safe and efficient way of treating diseases of the blood directly in patients. By allowing site-targeted gene intervention without homology-directed repair donor templates and DNA double-stranded breaks, the invention of prime editing fuels the exploration of alternatives to conventional recombination-based ex vivo genome editing of hematopoietic stem cells. Prime editing is as close as we get today to a true genome editing drug that does not require a separate DNA donor. However, to adapt the technology to perform in vivo gene correction, key challenges remain to be solved, such as identifying effective prime editing guide RNAs for clinical targets as well as developing efficient vehicles to deliver prime editors to stem cells in vivo. In this review, we summarize the current progress in delivery of prime editors both in vitro and in vivo and discuss future challenges that need to be adressed to allow in vivo prime editing as a cure for blood disorders.
Collapse
|
12
|
Jin S, Lin Q, Gao Q, Gao C. Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs). Nat Protoc 2023; 18:831-853. [PMID: 36434096 DOI: 10.1038/s41596-022-00773-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
Prime editors (PEs), which can install desired base edits without donor DNA or double-strand breaks, have been used in plants and can, in principle, accelerate crop improvement and breeding. However, their editing efficiency in plants is generally low. Optimizing the prime editing guide RNA (pegRNA) by designing the sequence on the basis of melting temperature, using dual-pegRNAs and engineering PEs have all been shown to enhance PE efficiency. In addition, an automated pegRNA design platform, PlantPegDesigner, has been developed on the basis of rice prime editing experimental data. In this protocol, we present detailed protocols for designing and optimizing pegRNAs using PlantPegDesigner, constructing engineered plant PE vectors with enhanced editing efficiency for prime editing, evaluating prime editing efficiencies using a reporter system and comparing the effectiveness and byproducts of PEs by deep amplicon sequencing. Using this protocol, researchers can construct optimized pegRNAs for prime editing in 4-7 d and obtain prime-edited rice or wheat plants within 3 months.
Collapse
Affiliation(s)
- Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiang Gao
- Qi Biodesign, Life Science Park, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
13
|
Chen PJ, Liu DR. Prime editing for precise and highly versatile genome manipulation. Nat Rev Genet 2023; 24:161-177. [PMID: 36344749 PMCID: PMC10989687 DOI: 10.1038/s41576-022-00541-1] [Citation(s) in RCA: 131] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Programmable gene-editing tools have transformed the life sciences and have shown potential for the treatment of genetic disease. Among the CRISPR-Cas technologies that can currently make targeted DNA changes in mammalian cells, prime editors offer an unusual combination of versatility, specificity and precision. Prime editors do not require double-strand DNA breaks and can make virtually any substitution, small insertion and small deletion within the DNA of living cells. Prime editing minimally requires a programmable nickase fused to a polymerase enzyme, and an extended guide RNA that both specifies the target site and templates the desired genome edit. In this Review, we summarize prime editing strategies to generate programmed genomic changes, highlight their limitations and recent developments that circumvent some of these bottlenecks, and discuss applications and future directions.
Collapse
Affiliation(s)
- Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
14
|
Future Perspectives of Prime Editing for the Treatment of Inherited Retinal Diseases. Cells 2023; 12:cells12030440. [PMID: 36766782 PMCID: PMC9913839 DOI: 10.3390/cells12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Inherited retinal diseases (IRD) are a clinically and genetically heterogenous group of diseases and a leading cause of blindness in the working-age population. Even though gene augmentation therapies have shown promising results, they are only feasible to treat a small number of autosomal recessive IRDs, because the size of the gene is limited by the vector used. DNA editing however could potentially correct errors regardless of the overall size of the gene and might also be used to correct dominant mutations. Prime editing is a novel CRISPR/Cas9 based gene editing tool that enables precise correction of point mutations, insertions, and deletions without causing double strand DNA breaks. Due to its versatility and precision this technology may be a potential treatment option for virtually all genetic causes of IRD. Since its initial description, the prime editing technology has been further improved, resulting in higher efficacy and a larger target scope. Additionally, progress has been achieved concerning the size-related delivery issue of the prime editor components. This review aims to give an overview of these recent advancements and discusses prime editing as a potential treatment for IRDs.
Collapse
|
15
|
Chen R, Cao Y, Liu Y, Zhao D, Li J, Cheng Z, Bi C, Zhang X. Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65. Nat Commun 2023; 14:257. [PMID: 36650182 PMCID: PMC9845348 DOI: 10.1038/s41467-023-35919-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Prime editing is a versatile gene editing tool that enables precise sequence changes of all types in the genome, but its application is rather limited by the editing efficiency. Here, we first apply the Suntag system to recruit the transcription factor P65 and enhance the desired editing outcomes in the prime editing system. Next, MS2 hairpins are used to recruit MS2-fused P65 and confirmed that the recruitment of the P65 protein could effectively improve the prime editing efficiency in both the PE3 and PE5 systems. Moreover, this suggests the increased editing efficiency is most likely associated with the induction of chromatin accessibility change by P65. In conclusion, we apply different systems to recruit P65 and enhance the prime editing efficiency of various PE systems. Furthermore, our work provides a variety of methods to work as protein scaffolds for screening target factors and thus supports further optimization of prime editing systems.
Collapse
Affiliation(s)
- Ronghao Chen
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Cao
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yajing Liu
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Zhihui Cheng
- College of Life Science, Nankai University, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| |
Collapse
|
16
|
Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
Collapse
Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
| |
Collapse
|
17
|
Huang Z, Liu G. Current advancement in the application of prime editing. Front Bioeng Biotechnol 2023; 11:1039315. [PMID: 36873365 PMCID: PMC9978821 DOI: 10.3389/fbioe.2023.1039315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Prime editing (PE) is a precise genome manipulation technology based on the "search and replace" approach of the CRISPR-Cas9 system, while it does not require the exogenous donor DNA and the DNA double-strand breaks (DSBs). Comparing the base editing technology, the editing scope of prime editing has been widely expanded. Prime editing has been successfully applied in a variety of plant cells, animal cells and the model microorganism Escherichia coli so far, and it has shown a good application potential in breeding and genomic functional study of animals and plants, disease treatment, and modification of the microbial strains. In this paper, the basic strategies of prime editing are briefly described, and its research progress is summarized and prospected from the application of multiple species. In addition, a variety of optimization strategies for improving its efficiency and specificity of prime editing are outlined.
Collapse
Affiliation(s)
- Zhangrao Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
18
|
Wang D, Fan X, Li M, Liu T, Lu P, Wang G, Li Y, Han J, Zhao J. Prime Editing in Mammals: The Next Generation of Precision Genome Editing. CRISPR J 2022; 5:746-768. [PMID: 36512351 DOI: 10.1089/crispr.2022.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The recently established prime editor (PE) system is regarded as next-generation gene-editing technology. This methodology can install any base-to-base change as well as insertions and deletions without the requirement for double-stranded break formation or donor DNA templates; thus, it offers more targeting flexibility and greater editing precision than conventional CRISPR-Cas systems or base editors. In this study, we introduce the basic principles of PE and then review its most recent progress in terms of editing versatility, specificity, and efficiency in mammals. Next, we summarize key considerations regarding the selection of PE variants, prime editing guide RNA (pegRNA) design rules, and the efficiency and accuracy evaluation of PE. Finally, we highlight and discuss how PE can assist in a wide range of biological studies and how it can be applied to make precise genomic corrections in animal models, which paves the way for curing human diseases.
Collapse
Affiliation(s)
- Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiude Fan
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tianbo Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Peng Lu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Guangxin Wang
- Shandong Innovation Center of Intelligent Diagnosis, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuan Li
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JunMing Han
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JiaJun Zhao
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| |
Collapse
|
19
|
Becklin KL, Draper GM, Madden RA, Kluesner MG, Koga T, Huang M, Weiss WA, Spector LG, Largaespada DA, Moriarity BS, Webber BR. Developing Bottom-Up Induced Pluripotent Stem Cell Derived Solid Tumor Models Using Precision Genome Editing Technologies. CRISPR J 2022; 5:517-535. [PMID: 35972367 PMCID: PMC9529369 DOI: 10.1089/crispr.2022.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genome and tissue engineering have spurred significant progress and opportunity for innovation in cancer modeling. Human induced pluripotent stem cells (iPSCs) are an established and powerful tool to study cellular processes in the context of disease-specific genetic backgrounds; however, their application to cancer has been limited by the resistance of many transformed cells to undergo successful reprogramming. Here, we review the status of human iPSC modeling of solid tumors in the context of genetic engineering, including how base and prime editing can be incorporated into "bottom-up" cancer modeling, a term we coined for iPSC-based cancer models using genetic engineering to induce transformation. This approach circumvents the need to reprogram cancer cells while allowing for dissection of the genetic mechanisms underlying transformation, progression, and metastasis with a high degree of precision and control. We also discuss the strengths and limitations of respective engineering approaches and outline experimental considerations for establishing future models.
Collapse
Affiliation(s)
- Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Garrett M. Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca A. Madden
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, La Jolla, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Miller Huang
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - William A. Weiss
- Departments of Neurology, Pediatrics, Neurosurgery, Brain Tumor Research Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; and Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - David A. Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|