Recent advances in CRISPR-based functional genomics for the study of disease-associated genetic variants
0
조회
0
다운로드
0
인용
0
참고문헌
초록
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.
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.
참고문헌 (95)
- Landrum, M. J., "ClinVar : public archive of interpretations of clinically relevant variants", Nucleic Acids Res, 44, pp.D862~D868 (2016)
- Tate, J. G., "COSMIC : the Catalogue Of Somatic Mutations In Cancer", Nucleic Acids Res, 47, pp.D941~D947 (2019)
- Visscher, P. M., "10 Years of GWAS Discovery : Biology, Function, and Trans lation", Am. J. Hum. Genet, 101, pp.5~22 (2017)
- Yang, J., "GCTA : a tool for genome-wide complex trait analysis", Am. J. Hum. Genet, 88, pp.76~82 (2011)
- Wang, J. Y., "CRISPR technology: A decade of genome editing is only the beginning", Science, 379, pp.eadd8643~ (2023)
- Hou, Z., "Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis", Proc. Natl Acad. Sci. USA, 110, pp.15644~15649 (2013)
- Ran, F. A., "In vivo genome editing using Staphylococcus aureus Cas9", Nature, 520, pp.186~191 (2015)
- Zetsche, B., "Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR Cas system", Cell, 163, pp.759~771 (2015)
- Hirano, H., "Structure and Engineering of Francisella novicida Cas9", Cell, 164, pp.950~961 (2016)
- Kim, E., "In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni", Nat. Commun, 8, pp.14500~ (2017)
- Agudelo, D., "Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9", Genome Res, 30, pp.107~117 (2020)
- Hu, Z., "A compact Cas9 ortholog from Staphylococcus Auricularis(SauriCas9)expands the DNA targeting scope", PLoS Biol, 18, pp.e3000686~ (2020)
- Wu, Z., "Programmed genome editing by a miniature CRISPR-Cas12f nucle ase", Nat. Chem. Biol, 17, pp.1132~1138 (2021)
- Kim, D. Y., "Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus", Nat. Biotechnol, 40, pp.94~102 (2022)
- Shalem, O., "High-throughput functional genomics using CRISPR-Cas9", Nat. Rev. Genet, 16, pp.299~311 (2015)
- Kweon, J., "High-throughput genetic screens using CRISPR-Cas9 system", Arch. Pharm. Res, 41, pp.875~884 (2018)
- Schadt, E. E., "A window into third-generation sequen cing", Hum. Mol. Genet, 19, pp.R227~R240 (2010)
- Deamer, D., "Three decades of nanopore sequencing", Nat. Biotechnol, 34, pp.518~524 (2016)
- Singh, M., "High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes", Nat. Commun, 10, pp.3120~ (2019)
- Kim, H. S., "Single-cell character ization of CRISPR-modified transcript isoforms with nanopore sequencing", Gen ome Biol, 22, pp.331~ (2021)
- Kim H. S., "Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells", Nat. Biotechnol (2023)[DOI]
- Al’Khafaji A. M., "High-throughput RNA isoform sequencing using pro grammed cDNA concatenation", Nat. Biotechnol (2023)[DOI]
- Klein, A. M., "Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells", Cell, 161, pp.1187~1201 (2015)
- Macosko, E. Z., "Highly Parallel Genome-wide Expression Profiling of Indivi dual Cells Using Nanoliter Droplets", Cell, 161, pp.1202~1214 (2015)
- Kleinstiver, B. P., "Engineered CRISPR-Cas9 nucleases with altered PAM spe cificities", Nature, 523, pp.481~485 (2015)
- Hu, J. H., "Evolved Cas9 variants with broad PAM compatibility and high DNA specificity", Nature, 556, pp.57~63 (2018)
- Nishimasu, H., "Engineered CRISPR-Cas9 nuclease with expanded targeting space", Science, 361, pp.1259~1262 (2018)
- Walton, R. T., "Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants", Science, 368, pp.290~296 (2020)
- Gao, L., "Engineered Cpf1 variants with altered PAM specificities", Nat. Bio technol, 35, pp.789~792 (2017)
- Kim, H., "A guide to genome engineering with programmable nucleases", Nat. Rev. Genet, 15, pp.321~334 (2014)
- Yeh, C. D., "Advances in genome editing through control of DNA repair pathways", Nat. Cell Biol, 21, pp.1468~1478 (2019)
- Heyer, W. D., "Regulation of homologous recombination in eukaryotes", Annu Rev. Genet, 44, pp.113~139 (2010)
- Moynahan, M. E., "Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis", Nat. Rev. Mol. Cell Biol, 11, pp.196~207 (2010)
- Kosicki, M., "Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements", Nat. Bio technol, 36, pp.765~771 (2018)
- Haapaniemi, E., "CRISPR-Cas9genome editing induces a p53-mediated DNA damage response", Nat. Med, 24, pp.927~930 (2018)
- Ihry, R. J., "p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells", Nat. Med, 24, pp.939~946 (2018)
- Lieber, M. R., "The mechanism of double-strand DNA break repair by the non homologous DNA end-joining pathway", Annu Rev. Biochem, 79, pp.181~211 (2010)
- Cong, L., "Multiplex genome engineering using CRISPR", Cas systems, 2013, pp.339, 819~823
- Torres, R., "Engineering human tumour-associated chromosomal transloca tions with the RNA-guided CRISPR-Cas9 system", Nat. Commun, 5, pp.3964~ (2014)
- Maddalo, D., "In vivo engineering of oncogenic chromosomal rearrange ments with the CRISPR", Cas9 system, 2014, pp.516, 423~427
- Huang, T. P., "Precision genome editing using cytosine and adenine base editors in mammalian cells", Nat. Protoc, 16, pp.1089~1128 (2021)
- Komor, A. C., "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage", Nature, 533, pp.420~424 (2016)
- Nishida, K., "Targeted nucleotide editing using hybrid prokaryotic and ver tebrate adaptive immune systems", Science, 353, pp.aaf8729~ (2016)
- Gaudelli, N. M., "Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage", Nature, 551, pp.464~471 (2017)
- Kurt, I. C., "CRISPR C-to-G base editors for inducing targeted DNA transver sions in human cells", Nat. Biotechnol, 39, pp.41~46 (2021)
- Zhao, D., "Glycosylase base editors enable C-to-A and C-to-G base changes", Nat. Biotechnol, 39, pp.35~40 (2021)
- Tong, H., "Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase", Nat. Biotechnol, 41, pp.1080~1084 (2023)
- Chen L., "Adenine transversion editors enable precise, efficient A*T-to-C*G base editing in mammalian cells and embryos", Nat Biotechnol (2023)[DOI]
- Rees, H. A., "Base editing : precision chemistry on the genome and transcriptome of living cells", Nat. Rev. Genet, 19, pp.770~788 (2018)
- Kuscu, C., "CRISPR-STOP : gene silencing through base-editing-induced non sense mutations", Nat. Methods, 14, pp.710~712 (2017)
- Billon, P., "CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons", Mol. Cell, 67, pp.1068~1079 (2017)
- Gapinske, M., "CRISPR-SKIP : programmable gene splicing with single base editors", Genome Biol, 19, pp.107~ (2018)
- Yuan, J., "Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase", Mol. Cell, 72, pp.380~394 (2018)
- Anzalone, A. V., "Search-and-replace genome editing without double-strand breaks or donor DNA", Nature, 576, pp.149~157 (2019)
- Chen, P. J., "Enhanced prime editing systems by manipulating cellular determinants of editing outcomes", Cell, 184, pp.5635~5652 (2021)
- Nelson, J. W., "Engineered pegRNAs improve prime editing efficiency", Nat. Biotechnol, 40, pp.402~410 (2022)
- Ferreira da Silva, J., "Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair", Nat. Commun, 13, pp.760~ (2022)
- Liu, P., "Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice", Nat. Commun, 12, pp.2121~ (2021)
- Velimirovic, M., "Peptide fusion improves prime editing efficiency", Nat. Commun, 13, pp.3512~ (2022)
- Song, M., "Generation of a more efficient prime editor 2 by addition of the Rad51 DNA-binding domain", Nat. Commun, 12, pp.5617~ (2021)
- Jang, G., "CRISPR prime editing for unconstrained correction of oncogenic KRAS variants", Commun. Biol, 6, pp.681~ (2023)
- Gibson, T. J., "The transience of transient overexpression", Nat. Methods, 10, pp.715~721 (2013)
- Liu, S. J., "CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells", Science, 355, pp.aah7111~ (2017)
- Frangoul, H., "CRISPR-Cas9 Gene Editing for Sickle Cell Disease and beta Thalassemia", N. Engl. J. Med, 384, pp.252~260 (2021)
- Korkmaz, G., "Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9", Nat. Biotechnol, 34, pp.192~198 (2016)
- Chavez, M., "Advances in CRISPR therapeutics", Nat. Rev. Nephrol, 19, pp.9~22 (2023)
- Koike-Yusa, H., "Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library", Nat. Biotechnol, 32, pp.267~273 (2014)
- Shalem, O., "Genome-scale CRISPR-Cas9 knockout screening in human cells", Science, 343, pp.84~87 (2014)
- Wang, T., "Genetic screens in human cells using the CRISPR-Cas9 system", Science, 343, pp.80~84 (2014)
- Zhou, Y., "High-throughput screening of a CRISPR", Cas9 library for functional genomics in human cells, 2014, pp.509, 487~491
- Kim, H. S., "Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection", Genome Res, 28, pp.859~868 (2018)
- Wang, C., "Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization", Proc. Natl Acad. Sci. USA, 116, pp.10842~10851 (2019)
- Dixit, A., "Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens", Cell, 167, pp.1853~1866 (2016)
- Jaitin, D. A., "Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq", Cell, 167, pp.1883~1896 (2016)
- Datlinger, P., "Pooled CRISPR screening with single-cell transcriptome read out", Nat. Methods, 14, pp.297~301 (2017)
- Replogle, J. M., "Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing", Nat. Biotechnol, 38, pp.954~961 (2020)
- Kim, H. S., "CRISPR", Cas9-mediated gene knockout screens and target iden tification via whole-genome sequencing uncover host genes required for picor navirus infection, 2017, pp.292, 10664~10671
- Findlay, G. M., "Saturation editing of genomic regions by multiplex homology-directed repair", Nature, 513, pp.120~123 (2014)
- Findlay, G. M., "Accurate classification of BRCA1 variants with saturation genome editing", Nature, 562, pp.217~222 (2018)
- Radford, E. J., "Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation", Nat. Commun, 14, pp.7702~ (2023)
- Kim, H. K., "SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance", Sci. Adv, 5, pp.eaax9249~ (2019)
- Kim, H. K., "High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells", Nat. Biomed. Eng, 4, pp.111~124 (2020)
- Kim, H. K., "Predicting the efficiency of prime editing guide RNAs in human cells", Nat. Biotechnol, 39, pp.198~206 (2021)
- Kim, N., "Deep learning models to predict the editing efficiencies and out comes of diverse base editors", Nat Biotechnol, 42, pp.484~497 (2024)
- Kim, N., "Prediction of the sequence-specific cleavage activity of Cas9 var iants", Nat. Biotechnol, 38, pp.1328~1336 (2020)
- Song, M., "Sequence-specific prediction of the efficiencies of adenine and cytosine base editors", Nat. Biotechnol, 38, pp.1037~1043 (2020)
- Yu, G., "Prediction of efficiencies for diverse prime editing systems in multiple cell types", Cell, 186, pp.2256~2272 (2023)
- Kweon, J., "A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants", Oncogene, 39, pp.30~35 (2020)
- Cuella-Martin, R., "Functional interrogation of DNA damage response variants with base editing screens", Cell, 184, pp.1081~1097 (2021)
- Hanna, R. E., "Massively parallel assessment of human variants with base editor screens", Cell, 184, pp.1064~1080 (2021)
- Huang, C., "Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction", Genome Biol, 22, pp.80~ (2021)
- Kim, Y., "High-throughput functional evaluation of human cancer-associated mutations using base editors", Nat. Biotechnol, 40, pp.874~884 (2022)
- Sanchez-Rivera, F. J., "Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide var iants", Nat. Biotechnol, 40, pp.862~873 (2022)
- Ursu, O., "Massively parallel phenotyping of coding variants in cancer with Perturb-seq", Nat. Biotechnol, 40, pp.896~905 (2022)
- Jun, S., "Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells", Commun. Biol, 3, pp.154~ (2020)
