Research Progress of CRISPR System in Translational Medicine

doi:10.13560/j.cnki.biotech.bull.1985.2020-0250

Abstract

Abstract:

CRISPR system is the most widely used technology for gene editing in the current scientific researches. In the post genomic era,CRISPR system is of great significance for gene function research,disease development mechanism and gene targeted drug research. At present,CRISPR/Cas9 editing technology has been used to successfully construct cell and biological models for clinical medical research. However,CRISPR/Cas9,as a powerful gene editing technology,is not only used for gene deletion or gene knock-in,but also applied in the gene high-throughput screening,research on disease caused by gene silencing,cross epigenetic modification activating gene expression,reversible interference of target gene expression and molecular diagnosis of pathogenic microorganism infectious diseases via the research and application of CRISPR/Cas9 in translational medicine in recent years,such as the screening system of CRISPR gene-knockout library,CRISPR/dCas9 gene activation system,CRISPR interference technology and CRISPR molecular diagnosis technology,etc.,which promotes the application and development of CRISPR in translational medicine research.

Key words: CRISPR/Cas9, CRISPR molecular diagnosis, CRISPR gene-knockout library, CRISPR activation system, CRISPR interference

YE Zhou-jie, WANG Xin-rui. Research Progress of CRISPR System in Translational Medicine[J]. Biotechnology Bulletin, 2020, 36(11): 188-197.

Figures/Tables 4

References 60

[1]	Yang F, Ge X, Gu F. Progress of next-generation targeted gene-editing techniques[J]. China Biotechnology, 2014,34(2):98-103.
[2]	Barrangou R, Fremaux C, Deveau H, et al. CRISPR provides acquired resistance against viruses in prokaryotes[J]. Science, 2007,315(5819):1709-1712. doi: 10.1126/science.1138140 URL pmid: 17379808
[3]	Jackson RN, Lavin M, Carter J, et al. Fitting CRISPR-associated Cas3 into the helicase family tree[J]. Current Opinion in Structural Biology, 2014,24:106-114. doi: 10.1016/j.sbi.2014.01.001 URL pmid: 24480304
[4]	Terns MP. CRISPR-Based Technologies:Impact of RNA-Targeting systems[J]. Molecular Cell, 2018,72(3):404-412. doi: 10.1016/j.molcel.2018.09.018 URL pmid: 30388409
[5]	Jiang F, Doudna JA. CRISPR-Cas9 structures and mechanisms[J]. Annual Review of Biophysics, 2017, 46(1):annurev-biophys-062215-010822.
[6]	Horii T, Hatada I. Genome engineering using the CRISPR/Cas system[J]. World Journal of Medical Genetics, 2014,4(3):69-76.
[7]	Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012,337(6096):816-821. doi: 10.1126/science.1225829 URL pmid: 22745249
[8]	Heler R, Samai P, Modell JW, et al. Cas9 specifies functional viral targets during CRISPR-Cas adaptation[J]. Nature, 2015,519(7542):199-202. doi: 10.1038/nature14245 URL pmid: 25707807
[9]	Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification[J]. Nature Biotechnology, 2014,32(6):577-582. doi: 10.1038/nbt.2909 URL
[10]	Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression[J]. Cell, 2013,152(5):1173-1183. doi: 10.1016/j.cell.2013.02.022 URL
[11]	Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013,339(6121):819-823. doi: 10.1126/science.1229223 URL
[12]	Luo X, He YX, Zhang C, et al. Trio deep-sequencing does not reveal unexpected off-target and on-target mutations in Cas9-edited rhesus monkeys[J]. Nature Communications, 2019,10(1):1-7. doi: 10.1038/s41467-018-07882-8 URL pmid: 30602773
[13]	Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea:versatile small RNAs for adaptive defense and regulation.[J]. Annual Review of Genetics, 2011,45(45):273-297. doi: 10.1146/annurev-genet-110410-132430 URL
[14]	Ran F, Hsu P, Lin CY, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity[J]. Cell, 2013,154(6):1380-1389. doi: 10.1016/j.cell.2013.08.021 URL pmid: 23992846
[15]	Yang S, Chang R, Yang H, et al. CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington’s disease[J]. The Journal of Clinical Investigation, 2017,127(7):2719-2724. doi: 10.1172/JCI92087 URL pmid: 28628038
[16]	Zhou Y, Sharma J, Ke Q, et al. Atypical behaviour and connectivity in SHANK3-mutant macaques[J]. Nature, 2019,570(7761):326-331. doi: 10.1038/s41586-019-1278-0 URL pmid: 31189958
[17]	Wu D, Hu D, Chen H, et al. Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer[J]. Nature 2018,559(7715):637-641 doi: 10.1038/s41586-018-0350-5 URL pmid: 30022161
[18]	Fraietta JA, Nobles CL, Sammons MA, et al. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells[J]. Nature, 2018,558(7709):307-312. doi: 10.1038/s41586-018-0178-z URL pmid: 29849141
[19]	Wang L, Li L, Ma Y, et al. Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies[J]. Cell Research, 2020: 1-3. doi: 10.1038/cr.1998.1 URL pmid: 9570012
[20]	Hille F, Richter H, Wong SP, et al. The biology of CRISPR-Cas:backward and forward[J]. Cell, 2018,172(6):1239-1259. doi: 10.1016/j.cell.2017.11.032 URL pmid: 29522745
[21]	Ma E, Harrington LB, O’Connell MR, et al. Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes[J]. Molecular Cell, 2015,60(3):398-407. URL pmid: 26545076
[22]	Zetsche B, Gootenberg JS, Abudayyeh OO, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 2015,163(3):759-771. doi: 10.1016/j.cell.2015.09.038 URL pmid: 26422227
[23]	Chen JS, Ma E, Harrington LB, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity[J]. Science, 2018,360(6387):436-439. doi: 10.1126/science.aar6245 URL pmid: 29449511
[24]	Woodman CBJ, Collins SI, Young LS. The natural history of cervical HPV infection:unresolved issues[J]. Nature Reviews Cancer, 2007,7(1):11-22. doi: 10.1038/nrc2050 URL pmid: 17186016
[25]	Zuo X, Fan C, Chen HY. Biosensing:CRISPR-powered diagnostics[J]. Nature Biomedical Engineering, 2017,1(6):1-2. doi: 10.1038/s41551-016-0001 URL
[26]	Abudayyeh OO, Gootenberg JS, Konermann S, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector[J]. Science, 2016, 353(6299):aaf5573. doi: 10.1126/science.aaf5573 URL pmid: 27256883
[27]	East-Seletsky A, O’Connell MR, Knight SC, et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection[J]. Nature, 2016,538(7624):270-273. doi: 10.1038/nature19802 URL pmid: 27669025
[28]	Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2[J]. Science, 2017,356(6336):438-442. doi: 10.1126/science.aam9321 URL pmid: 28408723
[29]	Myhrvold C, Freije CA, Gootenberg JS, et al. Field-deployable viral diagnostics using CRISPR-Cas13[J]. Science, 2018,360(6387):444-448. doi: 10.1126/science.aas8836 URL pmid: 29700266
[30]	Gootenberg JS, Abudayyeh OO, Kellner MJ, et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6[J]. Science, 2018,360(6387):439-444. doi: 10.1126/science.aaq0179 URL pmid: 29449508
[31]	Xu Z, Shi L, Wang Y, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome[J]. The Lancet Respiratory Medicine, 2020,8:420-422. doi: 10.1016/S2213-2600(20)30076-X URL pmid: 32085846
[32]	Freije CA, Myhrvold C, Boehm CK, et al. Programmable inhibition and detection of RNA viruses using Cas13[J]. Molecular cell, 2019,76(5):826-837. doi: 10.1016/j.molcel.2019.09.013 URL pmid: 31607545
[33]	Nguyen TM, Zhang Y, Pandolfi PP. Virus against virus:a potent-ial treatment for 2019-nCov(SARS-CoV-2)and other RNA viru-ses[J]. Cell Research, 2020. Doi: 1038/s41422-020-0290-0. doi: 10.1038/s41422-020-00422-4 URL pmid: 33051594
[34]	Zhou Y, Zhu S, Cai C, et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells[J]. Nature, 2014,509(7501):487-491. doi: 10.1038/nature13166 URL pmid: 24717434
[35]	Yang X, Boehm JS, Yang X, et al. A public genome-scale lentiviral expression library of human ORFs[J]. Nature Methods, 2011,8(8):659-661. doi: 10.1038/nmeth.1638 URL pmid: 21706014
[36]	Mohr SE, Smith JA, Shamu CE, et al. RNAi screening comes of age:improved techniques and complementary approaches[J]. Nature Reviews Molecular Cell Biology, 2014,15(9):591-600. doi: 10.1038/nrm3860 URL pmid: 25145850
[37]	Rana TM. Illuminating the silence:understanding the structure and function of small RNAs[J]. Nature Reviews Molecular Cell Biology, 2007,8(1):23-36. doi: 10.1038/nrm2085 URL pmid: 17183358
[38]	Sachse C, Krausz E, Krönke A, et al. High-throughput RNA interference strategies for target discovery and validation by using synthetic short interfering RNAs:functional genomics investigations of biological pathways[M] //Methods in enzymology. Academic Press, 2005,392:242-277.
[39]	Shalem O, Sanjana NE, Hartenian E, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells[J]. Science, 2014,343(6166):84-87. doi: 10.1126/science.1247005 URL pmid: 24336571
[40]	Han J, Perez JT, Chen C, et al. Genome-wide CRISPR/Cas9 screen identifies host factors essential for influenza virus replication[J]. Cell Reports, 2018,23(2):596-607. doi: 10.1016/j.celrep.2018.03.045 URL pmid: 29642015
[41]	Balboa D, Weltner, Eurola S, et al. Conditionally stabilized dCas9 activator for controlling gene expression in human cell reprogramming and differentiation[J]. Stem Cell Reports, 2015,5(3):448-459. doi: 10.1016/j.stemcr.2015.08.001 URL pmid: 26352799
[42]	Fujita T, Fujii H. Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation(enChIP)using CRISPR[J]. Biochemical and Biophysical Research Communications, 2013,439(1):132-136. doi: 10.1016/j.bbrc.2013.08.013 URL pmid: 23942116
[43]	Moosmann P, Georgiev O, Thiesen HJ, et al. Silencing of RNA polymerases II and III-dependent transcription by the KRAB protein domain of KOX1, a Krüppel-type zinc finger factor[J]. Biological Chemistry, 1997,378(7):669-678. doi: 10.1515/bchm.1997.378.7.669 URL pmid: 9278146
[44]	Liu SJ, Horlbeck MA, Cho SW, et al. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells[J]. Science, 2017, 355(6320):eaah7111.
[45]	Kearns NA, Pham H, Tabak B, et al. Functional annotation of native enhancers with a Cas9-histone demethylase fusion[J]. Nature Methods, 2015,12(5):401-403. doi: 10.1038/nmeth.3325 URL pmid: 25775043
[46]	Pfister SX, Ashworth A. Marked for death:targeting epigenetic changes in cancer[J]. Nature Reviews Drug Discovery, 2017,16(4):241. doi: 10.1038/nrd.2016.256 URL pmid: 28280262
[47]	Liao HK, Hatanaka F, Araoka T, et al. In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation[J]. Cell, 2017,171(7):1495-1507. doi: 10.1016/j.cell.2017.10.025 URL pmid: 29224783
[48]	Heerboth S, Lapinska K, Snyder N, et al. Use of epigenetic drugs in disease:an overview[J]. Genetics & Epigenetics, 2014, 6:GEG. S12270. 9-19. doi: 10.4137/GEG.S12270 URL pmid: 25512710
[49]	Maeder ML, Linder SJ, Cascio VM, et al. CRISPR RNA-guided activation of endogenous human genes[J]. Nature Methods, 2013,10(10):977-979. doi: 10.1038/NMETH.2598 URL pmid: 23892898
[50]	Hsu P, Lander E, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering[J]. Cell, 2014,157(6):1262-1278. doi: 10.1016/j.cell.2014.05.010 URL pmid: 24906146
[51]	Ji H, Jiang Z, Lu P, et al. Specific reactivation of latent HIV-1 by dCas9-SunTag-VP64-mediated guide RNA targeting the HIV-1 promoter[J]. Molecular Therapy, 2016,24(3):508-521. doi: 10.1038/mt.2016.7 URL pmid: 26775808
[52]	Liao HK, Hatanaka F, Araoka T, et al. In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation[J]. Cell, 2017,171(7):1495-1507. doi: 10.1016/j.cell.2017.10.025 URL pmid: 29224783
[53]	Dahlman JE, Abudayyeh OO, Joung J, et al. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease[J]. Nature Biotechnology, 2015,33(11):1159-1161. doi: 10.1038/nbt.3390 URL pmid: 26436575
[54]	Matharu N, Rattanasopha S, Tamura S, et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency[J]. Science, 2019, 363(6424):eaau0629. doi: 10.1126/science.aau0629 URL pmid: 30545847
[55]	Konermann S, Brigham MD, Trevino AE, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex[J]. Nature, 2015,517(7536):583-588. doi: 10.1038/nature14136 URL pmid: 25494202
[56]	Johannessen CM, Boehm JS, Kim SY, et al. COT drives resistance to RAF inhibition through MAP kinase pathway reactivation[J]. Nature, 2010,468(7326):968-972. doi: 10.1038/nature09627 URL pmid: 21107320
[57]	Musgrove EA, Sutherland RL . Biological determinants of endocrine resistance in breast cancer[J]. Nature Reviews Cancer, 2009,9(9):631-643. doi: 10.1038/nrc2713 URL pmid: 19701242
[58]	Heaton BE, Kennedy EM, Dumm RE, et al. A CRISPR activation screen identifies a pan-avian influenza virus inhibitory host factor[J]. Cell Reports, 2017,20(7):1503-1512. doi: 10.1016/j.celrep.2017.07.060 URL pmid: 28813663
[59]	Dahlman JE, Abudayyeh OO, Joung J, et al. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease[J]. Nature Biotechnology, 2015,33(11):1159-1163. doi: 10.1038/nbt.3390 URL pmid: 26436575
[60]	Schaefer KA, Wu WH, Colgan DF, et al. Unexpected mutations after CRISPR-Cas9 editing in vivo[J]. Nature Methods, 2017,14(6):547-548. doi: 10.1038/nmeth.4293 URL pmid: 28557981