Synthetic Biology Journal ›› 2022, Vol. 3 ›› Issue (1): 53-65.DOI: 10.12211/2096-8280.2021-046
• Invited Review • Previous Articles Next Articles
Fei SONG1,2, Yuchen LIU1,2, Zhiming CAI1,2, Weiren HUANG1,2
Received:
2021-04-15
Revised:
2021-11-24
Online:
2022-03-14
Published:
2022-02-28
Contact:
Weiren HUANG
宋斐1,2, 刘宇辰1,2, 蔡志明1,2, 黄卫人1,2
通讯作者:
黄卫人
作者简介:
基金资助:
CLC Number:
Fei SONG, Yuchen LIU, Zhiming CAI, Weiren HUANG. Construction of tumor gene circuits using CRISPR/Cas tool and their applications[J]. Synthetic Biology Journal, 2022, 3(1): 53-65.
宋斐, 刘宇辰, 蔡志明, 黄卫人. 基于CRISPR/Cas工具的肿瘤基因线路构建及应用[J]. 合成生物学, 2022, 3(1): 53-65.
Add to citation manager EndNote|Ris|BibTeX
URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2021-046
1 | HANAHAN D, WEINBERG R A. The hallmarks of cancer [J]. Cell, 2000, 100(1): 57-70. |
2 | BROPHY J A N, VOIGT C A. Principles of genetic circuit design[J]. Nature Methods, 2014, 11(5): 508-520. |
3 | ROYBAL K T, RUPP L J, MORSUT L, et al. Precision tumor recognition by T cells with combinatorial antigen-sensing circuits[J]. Cell, 2016, 164(4): 770-779. |
4 | NISSIM L, WU M R, PERY E, et al. Synthetic RNA-based immunomodulatory gene circuits for cancer immunotherapy[J]. Cell, 2017, 171(5): 1138-1150. |
5 | XIE M Q, YE H F, WANG H, et al. β-Cell-mimetic designer cells provide closed-loop glycemic control[J]. Science, 2016, 354(6317): 1296-1301. |
6 | ZETSCHE B, GOOTENBERG J S, ABUDAYYEH O O, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 2015, 163(3): 759-771. |
7 | TANG X, LOWDER L G, ZHANG T, et al. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants[J]. Nature Plants, 2017, 3: 17018. |
8 | YAMANO T, ZETSCHE B, ISHITANI R, et al. Structural basis for the canonical and non-canonical PAM recognition by CRISPR-Cpf1[J]. Molecular Cell, 2017, 67(4): 633-645. |
9 | WANG L P, WANG H J, LIU H Y, et al. Improved CRISPR-Cas12a-assisted one-pot DNA editing method enables seamless DNA editing[J]. Biotechnology and Bioengineering, 2019, 116(6): 1463-1474. |
10 | NIHONGAKI Y, OTABE T, UEDA Y, et al. A split CRISPR-Cpf1 platform for inducible genome editing and gene activation[J]. Nature Chemical Biology, 2019, 15(9): 882-888. |
11 | FREIJE C A, MYHRVOLD C, BOEHM C K, et al. Programmable inhibition and detection of RNA viruses using Cas13[J]. Molecular Cell, 2019, 76(5): 826-837. |
12 | YANG L Z, WANG Y, LI S Q, et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems[J]. Molecular Cell, 2019, 76(6): 981-997. |
13 | NANDAGOPAL N, ELOWITZ M B. Synthetic biology: Integrated gene circuits[J]. Science, 2011, 333(6047): 1244-1248. |
14 | FRIEDLAND A E, LU T K, WANG X, et al. Synthetic gene networks that count[J]. Science, 2009, 324(5931): 1199-1202. |
15 | DANINO T, MONDRAGÓN-PALOMINO O, TSIMRING L, et al. A synchronized quorum of genetic clocks[J]. Nature, 2010, 463(7279): 326-330. |
16 | NIELSEN J, KEASLING J D. Engineering cellular metabolism[J]. Cell, 2016, 164(6): 1185-1197. |
17 | GUPTA S, BRAM E E, WEISS R. Genetically programmable pathogen sense and destroy[J]. ACS Synthetic Biology, 2013, 2(12): 715-723. |
18 | CULLER S J, HOFF K G, SMOLKE C D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins[J]. Science, 2010, 330(6008): 1251-1255. |
19 | ZHAN H J, XIE H B, ZHOU Q, et al. Synthesizing a genetic sensor based on CRISPR-Cas9 for specifically killing p53-deficient cancer cells[J]. ACS Synthetic Biology, 2018, 7(7): 1798-1807. |
20 | MEGRAW M, CUMBIE J S, IVANCHENKO M G, et al. Small genetic circuits and microRNAs: Big players in polymerase II transcriptional control in plants[J]. Plant Cell, 2016, 28(2): 286-303. |
21 | JANSING J, SACK M, AUGUSTINE S M, et al. CRISPR/Cas9-mediated knockout of six glycosyltransferase genes in Nicotiana benthamiana for the production of recombinant proteins lacking β-1,2-xylose and core α-1,3-fucose[J]. Plant Biotechnology Journal, 2019, 17(2): 350-361. |
22 | NIHONGAKI Y, YAMAMOTO S, KAWANO F, et al. CRISPR-Cas9-based photoactivatable transcription system[J]. Chemistry & Biology, 2015, 22(2): 169-174. |
23 | LIN F, DONG L, WANG W M, et al. An efficient light-inducible P53 expression system for inhibiting proliferation of bladder cancer cell[J]. International Journal of Biological Sciences, 2016, 12(10): 1273-1278. |
24 | ZHOU X X, ZOU X Z, CHUNG H K, et al. A single-chain photoswitchable CRISPR-Cas9 architecture for light-inducible gene editing and transcription[J]. ACS Chemical Biology, 2018, 13(2): 443-448. |
25 | STROVAS T J, ROSENBERG A B, KUYPERS B E, et al. MicroRNA-based single-gene circuits buffer protein synthesis rates against perturbations[J]. ACS Synthetic Biology, 2014, 3(5): 324-331. |
26 | KIPNISS N H, DINGAL P C D P, ABBOTT T R, et al. Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system[J]. Nature Communications, 2017, 8(1): 2212. |
27 | KIANI S, BEAL J, EBRAHIMKHANI M R, et al. CRISPR transcriptional repression devices and layered circuits in mammalian cells[J]. Nature Methods, 2014, 11(7): 723-726. |
28 | WANG Y D, LIAO S Y, GUAN N Z, et al. A versatile genetic control system in mammalian cells and mice responsive to clinically licensed sodium ferulate[J]. Science Advances, 2020, 6(32): eabb9484. |
29 | ZHOU Q, ZHAN H, LIAO X, et al. A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits[J]. Cell Proliferation, 2019, 52(2): e12552. |
30 | SHAO J W, XUE S, YU G L, et al. Smartphone-controlled optogenetically engineered cells enable semiautomatic glucose homeostasis in diabetic mice[J]. Science Translational Medicine, 2017, 9(387): eaal2298. |
31 | YU Y H, WU X, GUAN N Z, et al. Engineering a far-red light-activated split-Cas9 system for remote-controlled genome editing of internal organs and tumors[J]. Science Advances, 2020, 6(28): eabb1777. |
32 | ZHANG Y, LING X Y, SU X X, et al. Optical control of a CRISPR/Cas9 system for gene editing by using photolabile crRNA[J]. Angewandte Chemie International Edtion, 2020, 59(47): 20895-20899. |
33 | ZOU R S, LIU Y, WU B, et al. Cas9 deactivation with photocleavable guide RNAs[J]. Molecular Cell, 2021, 81(7): 1553-1565. |
34 | BUBECK F, HOFFMANN M D, HARTEVELD Z, et al. Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9[J]. Nature Methods, 2018, 15(11): 924-927. |
35 | NISSIM L, BAR-ZIV R H. A tunable dual-promoter integrator for targeting of cancer cells[J]. Molecular Systems Biology, 2010, 6: 444. |
36 | XIE Z, WROBLEWSKA L, PROCHAZKA L, et al. Multi-input RNAi-based logic circuit for identification of specific cancer cells[J]. Science, 2011, 333(6047): 1307-1311. |
37 | LI Y Q, JIANG Y, CHEN H, et al. Modular construction of mammalian gene circuits using TALE transcriptional repressors[J]. Nature Chemical Biology, 2015, 11(3): 207-213. |
38 | MA D C, PENG S G, XIE Z. Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells[J]. Nature Communications, 2016, 7: 13056. |
39 | MORSUT L, ROYBAL K T, XIONG X, et al. Engineering customized cell sensing and response behaviors using synthetic Notch receptors[J]. Cell, 2016, 164(4): 780-791. |
40 | LIU Y C, ZHAN Y H, CHEN Z C, et al. Directing cellular information flow via CRISPR signal conductors[J]. Nature Methods, 2016, 13(11): 938-944. |
41 | LIU Y C, LI J F, CHEN Z C, et al. Synthesizing artificial devices that redirect cellular information at will[J]. eLife, 2018, 7: e31936. |
42 | STERNBERG S H, REDDING S, JINEK M, et al. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9[J]. Nature, 2014, 507(7490): 62-67. |
43 | CHENG A W, WANG H Y, YANG H, et al. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system[J]. Cell Research, 2013, 23(10): 1163-1171. |
44 | ZALATAN J G, LEE M E, ALMEIDA R, et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds[J]. Cell, 2015, 160(1/2): 339-350. |
45 | RAN F A, CONG L, YAN W X, et al. In vivo genome editing using Staphylococcus aureus Cas9[J]. Nature, 2015, 520(7546): 186-191. |
46 | BURSTEIN D, HARRINGTON L B, STRUTT S C, et al. New CRISPR-Cas systems from uncultivated microbes[J]. Nature, 2017, 542(7640): 237-241. |
47 | NISHIMASU H, RAN F A, HSU P D, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA[J]. Cell, 2014, 156(5): 935-949. |
48 | NISHIMASU H, CONG L, YAN W X, et al. Crystal structure of Staphylococcus aureus Cas9[J]. Cell, 2015, 162(5): 1113-1126. |
49 | STERNBERG S H, LAFRANCE B, KAPLAN M, et al. Conformational control of DNA target cleavage by CRISPR-Cas9[J]. Nature, 2015, 527(7576): 110-113. |
50 | LIU Y C, HAN J H, CHEN Z C, et al. Engineering cell signaling using tunable CRISPR-Cpf1-based transcription factors[J]. Nature Communications, 2017, 8: 2095. |
51 | KIANI S, CHAVEZ A, TUTTLE M, et al. Cas9 gRNA engineering for genome editing, activation and repression[J]. Nature Methods, 2015, 12(11): 1051-1054. |
52 | ZHAN H J, ZHOU Q, GAO Q J, et al. Multiplexed promoterless gene expression with CRISPReader[J]. Genome Biology, 2019, 20(1): 113. |
53 | WEI S, ZOU Q J, LAI S S, et al. Conversion of embryonic stem cells into extraembryonic lineages by CRISPR-mediated activators[J]. Scientific Reports, 2016, 6: 19648. |
54 | LIU Y C, HUANG W R, CAI Z M. Synthesizing and gate minigene circuits based on CRISPReader for identification of bladder cancer cells[J]. Nature Communications, 2020, 11: 5486. |
55 | KOPINSKI P K, SINGH L N, ZHANG S P, et al. Mitochondrial DNA variation and cancer[J]. Nature Reviews Cancer, 2021, 21(7): 431-445. |
56 | CHOUDHURY A R, SINGH K K. Mitochondrial determinants of cancer health disparities[J]. Seminars in Cancer Biology, 2017, 47: 125-146. |
57 | JO A, HAM S, LEE G H, et al. Efficient mitochondrial genome editing by CRISPR/Cas9[J]. Biomed Research International, 2015, 2015: 305716. |
58 | WANG G, SHIMADA E, ZHANG J, et al. Correcting human mitochondrial mutations with targeted RNA import[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(13): 4840-4845. |
59 | GAMMAGE P A, MORAES C T, MINCZUK M. Mitochondrial genome engineering: the revolution may not be CRISPR-ized[J]. Trends in Genetics, 2018, 34(2): 101-110. |
60 | SMIRNOV A, TARASSOV I, MAGER-HECKEL A M, et al. Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria[J]. RNA, 2008, 14(4): 749-759. |
61 | YANG X B, JIANG J C, LI Z Y, et al. Strategies for mitochondrial gene editing[J]. Computational and Structural Biotechnology Journal, 2021, 19: 3319-3329. |
62 | YOO B C, YADAV N S, OROZCO E M JR, et al. Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts[J]. PeerJ, 2020, 8: e8362. |
63 | YUAN P Y, MAO X, WU X F, et al. Mitochondria-targeting, intracellular delivery of native proteins using biodegradable silica nanoparticles[J]. Angewandte Chemie International Edtion, 2019, 58(23): 7657-7661. |
64 | TORCHILIN V P. Recent approaches to intracellular delivery of drugs and DNA and organelle targeting[J]. Annual Review of Biomedical Engineering, 2006, 8: 343-375. |
65 | HADDAD S, ABÁNADES LÁZARO I, FANTHAM M, et al. Design of a functionalized metal-organic framework system for enhanced targeted delivery to mitochondria[J]. Journal of the American Chemical Society, 2020, 142(14): 6661-6674. |
66 | LOUTRE R, HECKEL A M, SMIRNOVA A, et al. Can mitochondrial DNA Be CRISPRized: Pro and Contra[J]. IUBMB Life, 2018, 70(12): 1233-1239. |
67 | BIAN W P, CHEN Y L, LUO J J, et al. Knock-in strategy for editing human and zebrafish mitochondrial DNA using Mito-CRISPR/Cas9 system[J]. ACS Synthetic Biology, 2019, 8(4): 621-632. |
68 | SWARTS D C, HEGGE J W, HINOJO I, et al. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA[J]. Nucleic Acids Research, 2015, 43(10): 5120-5129. |
69 | DUNBAR C E, HIGH K A, JOUNG J K, et al. Gene therapy comes of age[J]. Science, 2018, 359(6372): eaan4672. |
70 | GRIMM D, BÜNING H. Small but increasingly mighty: latest advances in AAV vector research, design, and evolution[J]. Human Gene Therapy, 2017, 28(11): 1075-1086. |
71 | LENIS T L, SARFARE S, JIANG Z C, et al. Complement modulation in the retinal pigment epithelium rescues photoreceptor degeneration in a mouse model of Stargardt disease[J]. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(15): 3987-3992. |
72 | KAUFMAN H L, KOHLHAPP F J, ZLOZA A. Oncolytic viruses: a new class of immunotherapy drugs[J]. Nature Reviews Drug Discovery, 2015, 14(9): 642-662. |
73 | YOON A R, JUNG B K, CHOI E, et al. CRISPR-Cas12a with an oAd induces precise and cancer-specific genomic reprogramming of EGFR and efficient tumor regression[J]. Molecular Therapy, 2020, 28(10): 2286-2296. |
74 | PHELPS M P, YANG H, PATEL S, et al. Oncolytic virus-mediated RAS targeting in rhabdomyosarcoma[J]. Molecular Therapy-Oncolytics, 2018, 11: 52-61. |
75 | HUANG H Y, LIU Y Q, LIAO W X, et al. Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy[J]. Nature Communications, 2019, 10: 4801. |
76 | SEGEL M, LASH B, SONG J W, et al. Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery[J]. Science, 2021, 373(6557): 882-889. |
77 | SHIN J, JIANG F G, LIU J J, et al. Disabling Cas9 by an anti-CRISPR DNA mimic[J]. Science Advances, 2017, 3(7): e1701620. |
78 | CHEN J S, DAGDAS Y S, KLEINSTIVER B P, et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy[J]. Nature, 2017, 550(7676): 407-410. |
79 | HARRINGTON L B, DOXZEN K W, MA E, et al. A broad-spectrum inhibitor of CRISPR-Cas9[J]. Cell, 2017, 170(6): 1224-1233.e1215. |
[1] | Mengdan MA, Mengyu SHANG, Yuchen LIU. Application and prospect of CRISPR-Cas9 system in tumor biology [J]. Synthetic Biology Journal, 2023, 4(4): 703-719. |
[2] | Ke XU, Jingnan WANG, Chun LI. Intelligent microbial cell factory with tolerance for green biological manufacturing [J]. Synthetic Biology Journal, 2020, 1(4): 427-439. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||