CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells
Abstract
:1. Introduction
2. Techniques for Single and Multiplexed Gene Manipulation of T Cells
2.1. Single Gene Knockouts
2.2. Multiplexed Knockouts
2.3. Single Gene Knockins
2.4. Multiplexed Gene Knockins
3. Techniques for Pooled Genetic Manipulation
3.1. Pooled Knockout Screens
3.2. Pooled Knockin Screens
4. Clinical Applications of Edited Primary T Cells
4.1. Editing of T Cells for Cancer Immunotherapy
4.2. Editing of T Cells for Antiretroviral Therapies
5. Summary and Future Directions
Funding
Acknowledgments
Conflicts of Interest
References
- Chaplin, D.D. Overview of the immune response. J. Allergy Clin. Immunol. 2010, 125, S3–S23. [Google Scholar] [CrossRef] [PubMed]
- Gaud, G.; Lesourne, R.; Love, P.E. Regulatory mechanisms in T cell receptor signalling. Nat. Rev. Immunol. 2018, 18, 485–497. [Google Scholar] [CrossRef] [PubMed]
- Fuertes Marraco, S.A.; Neubert, N.J.; Verdeil, G.; Speiser, D.E. Inhibitory Receptors Beyond T Cell Exhaustion. Front. Immunol. 2015, 6, 310. [Google Scholar] [CrossRef] [PubMed]
- Todryk, S.; Jozwik, A.; de Havilland, J.; Hester, J. Emerging Cellular Therapies: T Cells and Beyond. Cells 2019, 8, 284. [Google Scholar] [CrossRef] [Green Version]
- Sambi, M.; Bagheri, L.; Szewczuk, M.R. Current Challenges in Cancer Immunotherapy: Multimodal Approaches to Improve Efficacy and Patient Response Rates. J. Oncol. 2019, 2019, 4508794. [Google Scholar] [CrossRef] [Green Version]
- Torikai, H.; Reik, A.; Liu, P.-Q.; Zhou, Y.; Zhang, L.; Maiti, S.; Huls, H.; Miller, J.C.; Kebriaei, P.; Rabinovich, B.; et al. A foundation for universal T-cell based immunotherapy: T cells engineered to express a CD19-specific chimeric-antigen-receptor and eliminate expression of endogenous TCR. Blood 2012, 119, 5697–5705. [Google Scholar] [CrossRef] [Green Version]
- Osborn, M.J.; Webber, B.R.; Knipping, F.; Lonetree, C.L.; Tennis, N.; DeFeo, A.P.; McElroy, A.N.; Starker, C.G.; Lee, C.; Merkel, S.; et al. Evaluation of TCR gene editing achieved by TALENs, CRISPR/Cas9, and megaTAL nucleases. Mol. Ther. 2016, 24, 570–581. [Google Scholar] [CrossRef] [Green Version]
- Berdien, B.; Mock, U.; Atanackovic, D.; Fehse, B. TALEN-mediated editing of endogenous T-cell receptors facilitates efficient reprogramming of T lymphocytes by lentiviral gene transfer. Gene Ther. 2014, 21, 539–548. [Google Scholar] [CrossRef]
- Gaj, T.; Sirk, S.J.; Shui, S.-L.; Liu, J. Genome-Editing Technologies: Principles and Applications. Cold Spring Harb. Perspect. Biol. 2016, 8, a023754. [Google Scholar] [CrossRef] [Green Version]
- Doudna, J.A.; Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 2014, 346, 1258096. [Google Scholar] [CrossRef]
- Dominguez, A.A.; Lim, W.A.; Qi, L.S. Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 2016, 17, 5–15. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yeo, N.C.; Chavez, A.; Lance-Byrne, A.; Chan, Y.; Menn, D.; Milanova, D.; Kuo, C.C.; Guo, X.; Sharma, S.; Tung, A.; et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat. Methods 2018, 15, 611–616. [Google Scholar] [CrossRef] [PubMed]
- Anzalone, A.V.; Koblan, L.W.; Liu, D.R. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 2020, 38, 824–844. [Google Scholar] [CrossRef] [PubMed]
- Pickar-Oliver, A.; Gersbach, C.A. The next generation of CRISPR–Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 2019, 20, 490–507. [Google Scholar] [CrossRef] [PubMed]
- Wang, W.; Ye, C.; Liu, J.; Zhang, D.; Kimata, J.T.; Zhou, P. CCR5 gene disruption via lentiviral vectors expressing Cas9 and single guided RNA renders cells resistant to HIV-1 infection. PLoS ONE 2014, 9, e0115987. [Google Scholar] [CrossRef] [Green Version]
- Seki, A.; Rutz, S. Optimized RNP transfection for highly efficient CRI SPR/Cas9-mediated gene knockout in primary T cells. J. Exp. Med. 2018, 215, 985–997. [Google Scholar] [CrossRef]
- Yi, G.; Choi, J.G.; Bharaj, P.; Abraham, S.; Dang, Y.; Kafri, T.; Alozie, O.; Manjunath, M.N.; Shankar, P. CCR5 gene editing of resting CD4+ T cells by transient ZFN expression from HIV envelope pseudotyped nonintegrating lentivirus confers HIV-1 resistance in humanized mice. Mol. Therapy Nucleic Acids 2014, 3, e198. [Google Scholar] [CrossRef]
- Vella, A.; Teague, T.K.; Ihle, J.; Kappler, J.; Marrack, P. Interleukin 4 (IL-4) or IL-7 prevents the death of resting T cells: Stat6 is probably not required for the effect of IL-4. J. Exp. Med. 1997, 186, 325–330. [Google Scholar] [CrossRef] [Green Version]
- Kishimoto, H.; Sprent, J. Strong TCR ligation without costimulation causes rapid onset of Fas-dependent apoptosis of naive murine CD4+ T cells. J. Immunol. 1999, 163, 1817–1826. [Google Scholar]
- Schumann, K.; Lin, S.; Boyer, E.; Simeonov, D.R.; Subramaniam, M.; Gate, R.E.; Haliburton, G.E.; Ye, C.J.; Bluestone, J.A.; Doudna, J.A.; et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc. Natl. Acad. Sci. USA 2015, 112, 10437–10442. [Google Scholar] [CrossRef] [Green Version]
- Ren, J.; Liu, X.; Fang, C.; Jiang, S.; June, C.H.; Zhao, Y. Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition. Clin. Cancer Res. 2017, 23, 2255–2266. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- DeWitt, M.A.; Magis, W.; Bray, N.L.; Wang, T.; Berman, J.R.; Urbinati, F.; Heo, S.J.; Mitros, T.; Muñoz, D.P.; Boffelli, D.; et al. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci. Transl. Med. 2016, 8, 360ra134. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vakulskas, C.A.; Dever, D.P.; Rettig, G.R.; Turk, R.; Jacobi, A.M.; Collingwood, M.A.; Bode, N.M.; McNeill, M.S.; Yan, S.; Camarena, J.; et al. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nat. Med. 2018, 24, 1216–1224. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Haapaniemi, E.; Botla, S.; Persson, J.; Schmierer, B.; Taipale, J. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat. Med. 2018, 24, 927–930. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Loughran, G.; Chou, M.-Y.; Ivanov, I.P.; Jungreis, I.; Kellis, M.; Kiran, A.M.; Baranov, P.V.; Atkins, J.F. Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Res. 2014, 42, 8928–8938. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Webber, B.R.; Lonetree, C.L.; Kluesner, M.G.; Johnson, M.J.; Pomeroy, E.J.; Diers, M.D.; Lahr, W.S.; Draper, G.M.; Slipek, N.J.; Smeester, B.S.; et al. Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors. Nat. Commun. 2019, 10, 5222. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hendel, A.; Bak, R.O.; Clark, J.T.; Kennedy, A.B.; Ryan, D.E.; Roy, S.; Steinfeld, I.; Lunstad, B.D.; Kaiser, R.J.; Wilkens, A.B.; et al. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat. Biotechnol. 2015, 33, 985–989. [Google Scholar] [CrossRef]
- Eyquem, J.; Mansilla-Soto, J.; Giavridis, T.; Van Der Stegen, S.J.C.; Hamieh, M.; Cunanan, K.M.; Odak, A.; Gönen, M.; Sadelain, M. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 2017, 543, 113–117. [Google Scholar] [CrossRef] [Green Version]
- Roth, T.L.; Puig-Saus, C.; Yu, R.; Shifrut, E.; Carnevale, J.; Li, P.J.; Hiatt, J.; Saco, J.; Krystofinski, P.; Li, H.; et al. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature 2018, 559, 405–409. [Google Scholar] [CrossRef]
- Su, S.; Hu, B.; Shao, J.; Shen, B.; Du, J.; Du, Y.; Zhou, J.; Yu, L.; Zhang, L.; Chen, F.; et al. CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients. Sci. Rep. 2016, 6, 20070. [Google Scholar] [CrossRef] [Green Version]
- Mandal, P.K.; Ferreira, L.M.R.; Collins, R.; Meissner, T.B.; Boutwell, C.L.; Friesen, M.; Vrbanac, V.; Garrison, B.S.; Stortchevoi, A.; Bryder, D.; et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell 2014, 15, 643–652. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Beil-Wagner, J.; Dössinger, G.; Schober, K.; Vom Berg, J.; Tresch, A.; Grandl, M.; Palle, P.; Mair, F.; Gerhard, M.; Becher, B.; et al. T cell-specific inactivation of mouse CD2 by CRISPR/Cas9. Sci. Rep. 2016, 6, 21377. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Platt, R.J.; Chen, S.; Zhou, Y.; Yim, M.J.; Swiech, L.; Kempton, H.R.; Dahlman, J.E.; Parnas, O.; Eisenhaure, T.M.; Jovanovic, M.; et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 2014, 159, 440–455. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- LaFleur, M.W.; Nguyen, T.H.; Coxe, M.A.; Yates, K.B.; Trombley, J.D.; Weiss, S.A.; Brown, F.D.; Gillis, J.E.; Coxe, D.J.; Doench, J.G.; et al. A CRISPR-Cas9 delivery system for in vivo screening of genes in the immune system. Nat. Commun. 2019, 10, 1668. [Google Scholar] [CrossRef] [Green Version]
- Chu, V.T.; Graf, R.; Wirtz, T.; Weber, T.; Favret, J.; Li, X.; Petsch, K.; Tran, N.T.; Sieweke, M.H.; Berek, C.; et al. Efficient CRISPR-mediated mutagenesis in primary immune cells using CrispRGold and a C57BL/6 Cas9 transgenic mouse line. Proc. Natl. Acad. Sci. USA 2016, 113, 12514–12519. [Google Scholar] [CrossRef] [Green Version]
- Nüssing, S.; House, I.G.; Kearney, C.J.; Chen, A.X.Y.; Vervoort, S.J.; Beavis, P.A.; Oliaro, J.; Johnstone, R.W.; Trapani, J.A.; Parish, I.A. Efficient CRISPR/Cas9 Gene Editing in Uncultured Naive Mouse T Cells for In Vivo Studies. J. Immunol. 2020, 204, 2308–2315. [Google Scholar] [CrossRef]
- Cong, L.; Ran, F.A.; Cox, D.; Lin, S.; Barretto, R.; Habib, N.; Hsu, P.D.; Wu, X.; Jiang, W.; Marraffini, L.A.; et al. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339, 819–823. [Google Scholar] [CrossRef] [Green Version]
- Dai, X.; Park, J.J.; Du, Y.; Kim, H.R.; Wang, G.; Errami, Y.; Chen, S. One-step generation of modular CAR-T cells with AAV–Cpf1. Nat. Methods 2019, 16, 247–254. [Google Scholar] [CrossRef]
- McCarty, N.S.; Graham, A.E.; Studená, L.; Ledesma-Amaro, R. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat. Commun. 2020, 11, 1281. [Google Scholar] [CrossRef]
- Liu, X.; Zhang, Y.; Cheng, C.; Cheng, A.W.; Zhang, X.; Li, N.; Xia, C.; Wei, X.; Liu, X.; Wang, H. CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells. Cell Res. 2017, 27, 154–157. [Google Scholar] [CrossRef]
- Ren, J.; Zhang, X.; Liu, X.; Fang, C.; Jiang, S.; June, C.H.; Zhao, Y. A versatile system for rapid multiplex genome-edited CAR T cell generation. Oncotarget 2017, 8, 17002–17011. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Qasim, W.; Zhan, H.; Samarasinghe, S.; Adams, S.; Amrolia, P.; Stafford, S.; Butler, K.; Rivat, C.; Wright, G.; Somana, K.; et al. Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells. Sci. Transl. Med. 2017, 9, eaaj2013. [Google Scholar] [CrossRef] [PubMed]
- Poirot, L.; Philip, B.; Schiffer-Mannioui, C.; Le Clerre, D.; Chion-Sotinel, I.; Derniame, S.; Potrel, P.; Bas, C.; Lemaire, L.; Galetto, R.; et al. Multiplex Genome-Edited T-cell Manufacturing Platform for “Off-the-Shelf” Adoptive T-cell Immunotherapies. Cancer Res. 2015, 75, 3853–3864. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gaudelli, N.M.; Lam, D.K.; Rees, H.A.; Solá-Esteves, N.M.; Barrera, L.A.; Born, D.A.; Edwards, A.; Gehrke, J.M.; Lee, S.J.; Liquori, A.J.; et al. Directed evolution of adenine base editors with increased activity and therapeutic application. Nat. Biotechnol. 2020, 38, 892–900. [Google Scholar] [CrossRef]
- Lee, H.K.; Smith, H.E.; Liu, C.; Willi, M.; Hennighausen, L. Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos. Commun. Biol. 2020, 3, 19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zuo, E.; Sun, Y.; Wei, W.; Yuan, T.; Ying, W.; Sun, H.; Yuan, L.; Steinmetz, L.M.; Li, Y.; Yang, H. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 2019, 364, 289–292. [Google Scholar] [CrossRef] [PubMed]
- Jin, S.; Zong, Y.; Gao, Q.; Zhu, Z.; Wang, Y.; Qin, P.; Liang, C.; Wang, D.; Qiu, J.-L.; Zhang, F.; et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 2019, 364, 292–295. [Google Scholar] [CrossRef]
- Kornete, M.; Marone, R.; Jeker, L.T. Highly Efficient and Versatile Plasmid-Based Gene Editing in Primary T Cells. J. Immunol. 2018, 200, 2489–2501. [Google Scholar] [CrossRef] [Green Version]
- Xu, C.L.; Ruan, M.Z.C.; Mahajan, V.B.; Tsang, S.H. Viral delivery systems for crispr. Viruses 2019, 11, 28. [Google Scholar] [CrossRef] [Green Version]
- Li, K.; Wang, G.; Andersen, T.; Zhou, P.; Pu, W.T. Optimization of genome engineering approaches with the CRISPR/Cas9 system. PLoS ONE 2014, 9, e105779. [Google Scholar] [CrossRef]
- Boutin, S.; Monteilhet, V.; Veron, P.; Leborgne, C.; Benveniste, O.; Montus, M.F.; Masurier, C. Prevalence of serum IgG and neutralizing factors against adeno-associated virus (AAV) types 1, 2, 5, 6, 8, and 9 in the healthy population: Implications for gene therapy using AAV vectors. Hum. Gene Ther. 2010, 21, 704–712. [Google Scholar] [CrossRef]
- Herzog, R.W. Hemophilia Gene Therapy: Caught between a Cure and an Immune Response. Mol. Therapy 2015, 23, 1411–1412. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mingozzi, F.; High, K.A. Immune responses to AAV vectors: Overcoming barriers to successful gene therapy. Blood 2013, 122, 23–36. [Google Scholar] [CrossRef] [PubMed]
- Moreno-Mateos, M.A.; Fernandez, J.P.; Rouet, R.; Vejnar, C.E.; Lane, M.A.; Mis, E.; Khokha, M.K.; Doudna, J.A.; Giraldez, A.J. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat. Commun. 2017, 8, 2024. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zetsche, B.; Gootenberg, J.S.; Abudayyeh, O.O.; Slaymaker, I.M.; Makarova, K.S.; Essletzbichler, P.; Volz, S.E.; Joung, J.; Van Der Oost, J.; Regev, A.; et al. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell 2015, 163, 759–771. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Nguyen, D.N.; Roth, T.L.; Li, P.J.; Chen, P.A.; Apathy, R.; Mamedov, M.R.; Vo, L.T.; Tobin, V.R.; Goodman, D.; Shifrut, E.; et al. Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency. Nat. Biotechnol. 2020, 38, 44–49. [Google Scholar] [CrossRef] [PubMed]
- Gwiazda, K.S.; Grier, A.E.; Sahni, J.; Burleigh, S.M.; Martin, U.; Yang, J.G.; Popp, N.A.; Krutein, M.C.; Khan, I.F.; Jacoby, K.; et al. High efficiency CRISPR/Cas9-mediated gene editing in primary human T-cells using mutant adenoviral E4orf6/E1b55k “Helper” proteins. Mol. Ther. 2016, 24, 1570–1580. [Google Scholar] [CrossRef] [Green Version]
- Chu, V.T.; Weber, T.; Wefers, B.; Wurst, W.; Sander, S.; Rajewsky, K.; Kühn, R. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 2015, 33, 543–548. [Google Scholar] [CrossRef] [Green Version]
- Yu, C.; Liu, Y.; Ma, T.; Liu, K.; Xu, S.; Zhang, Y.; Liu, H.; La Russa, M.; Xie, M.; Ding, S.; et al. Small molecules enhance crispr genome editing in pluripotent stem cells. Cell Stem Cell 2015, 16, 142–147. [Google Scholar] [CrossRef] [Green Version]
- Maruyama, T.; Dougan, S.K.; Truttmann, M.C.; Bilate, A.M.; Ingram, J.R.; Ploegh, H.L. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 2015, 33, 538–542. [Google Scholar] [CrossRef]
- Wienert, B.; Nguyen, D.N.; Guenther, A.; Feng, S.J.; Locke, M.N.; Wyman, S.K.; Shin, J.; Kazane, K.R.; Gregory, G.L.; Carter, M.A.M.; et al. Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. Nat. Commun. 2020, 11, 2109. [Google Scholar] [CrossRef] [PubMed]
- Chen, R.; Bélanger, S.; Frederick, M.A.; Li, B.; Johnston, R.J.; Xiao, N.; Liu, Y.C.; Sharma, S.; Peters, B.; Rao, A.; et al. In vivo RNA interference screens identify regulators of antiviral CD4+ and CD8+ T cell differentiation. Immunity 2014, 41, 325–338. [Google Scholar] [CrossRef] [Green Version]
- Zhou, P.; Shaffer, D.R.; Alvarez Arias, D.A.; Nakazaki, Y.; Pos, W.; Torres, A.J.; Cremasco, V.; Dougan, S.K.; Cowley, G.S.; Elpek, K.; et al. In vivo discovery of immunotherapy targets in the tumour microenvironment. Nature 2014, 506, 52–57. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hanna, R.E.; Doench, J.G. Design and analysis of CRISPR–Cas experiments. Nat. Biotechnol. 2020, 38, 813–823. [Google Scholar] [CrossRef] [PubMed]
- Shifrut, E.; Carnevale, J.; Tobin, V.; Roth, T.L.; Woo, J.M.; Bui, C.T.; Li, P.J.; Diolaiti, M.E.; Ashworth, A.; Marson, A. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell 2018, 175, 1958–1971. [Google Scholar] [CrossRef] [Green Version]
- Datlinger, P.; Rendeiro, A.F.; Schmidl, C.; Krausgruber, T.; Traxler, P.; Klughammer, J.; Schuster, L.C.; Kuchler, A.; Alpar, D.; Bock, C. Pooled CRISPR screening with single-cell transcriptome readout. Nat. Methods 2017, 14, 297–301. [Google Scholar] [CrossRef] [Green Version]
- Dixit, A.; Parnas, O.; Li, B.; Chen, J.; Fulco, C.P.; Jerby-Arnon, L.; Marjanovic, N.D.; Dionne, D.; Burks, T.; Raychowdhury, R.; et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell 2016, 167, 1853–1866. [Google Scholar] [CrossRef]
- Ting, P.Y.; Parker, A.E.; Lee, J.S.; Trussell, C.; Sharif, O.; Luna, F.; Federe, G.; Barnes, S.W.; Walker, J.R.; Vance, J.; et al. Guide Swap enables genome-scale pooled CRISPR-Cas9 screening in human primary cells. Nat. Methods 2018, 15, 941–946. [Google Scholar] [CrossRef]
- Dong, M.B.; Wang, G.; Chow, R.D.; Ye, L.; Zhu, L.; Dai, X.; Park, J.J.; Kim, H.R.; Errami, Y.; Guzman, C.D.; et al. Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Cell 2019, 178, 1189–1204. [Google Scholar] [CrossRef]
- Ye, L.; Park, J.J.; Dong, M.B.; Yang, Q.; Chow, R.D.; Peng, L.; Du, Y.; Guo, J.; Dai, X.; Wang, G.; et al. In vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nat. Biotechnol. 2019, 37, 1302–1313. [Google Scholar] [CrossRef]
- Henriksson, J.; Chen, X.; Gomes, T.; Ullah, U.; Meyer, K.B.; Miragaia, R.; Duddy, G.; Pramanik, J.; Yusa, K.; Lahesmaa, R.; et al. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019, 176, 882–896. [Google Scholar] [CrossRef] [PubMed]
- Cortez, J.T.; Montauti, E.; Shifrut, E.; Gatchalian, J.; Zhang, Y.; Shaked, O.; Xu, Y.; Roth, T.L.; Simeonov, D.R.; Zhang, Y.; et al. CRISPR screen in regulatory T cells reveals modulators of Foxp3. Nature 2020, 582, 416–420. [Google Scholar] [CrossRef]
- Roth, T.L.; Li, P.J.; Blaeschke, F.; Nies, J.F.; Apathy, R.; Mowery, C.; Yu, R.; Nguyen, M.L.T.; Lee, Y.; Truong, A.; et al. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies. Cell 2020, 181, 728–744. [Google Scholar] [CrossRef] [PubMed]
- Xia, A.; Zhang, Y.; Xu, J.; Yin, T.; Lu, X.-J. T Cell Dysfunction in Cancer Immunity and Immunotherapy. Front. Immunol. 2019, 10, 1719. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bailey, S.R.; Maus, M.V. Gene editing for immune cell therapies. Nat. Biotechnol. 2019, 37, 1425–1434. [Google Scholar] [CrossRef] [PubMed]
- Cornu, T.I.; Mussolino, C.; Cathomen, T. Refining strategies to translate genome editing to the clinic. Nat. Med. 2017, 23, 415–423. [Google Scholar] [CrossRef]
- Porteus, M.H. A new class of medicines through DNA editing. N. Engl. J. Med. 2019, 380, 947–959. [Google Scholar] [CrossRef]
- Gallegos, A.M.; Xiong, H.; Leiner, I.M.; Sušac, B.; Glickman, M.S.; Pamer, E.G.; Van Heijst, J.W.J. Control of T cell antigen reactivity via programmed TCR downregulation. Nat. Immunol. 2016, 17, 379–386. [Google Scholar] [CrossRef]
- Legut, M.; Dolton, G.; Mian, A.A.; Ottmann, O.G.; Sewell, A.K. CRISPR-mediated TCR replacement generates superior anticancer transgenic t cells. Blood 2018, 131, 311–322. [Google Scholar] [CrossRef] [Green Version]
- Schober, K.; Müller, T.R.; Gökmen, F.; Grassmann, S.; Effenberger, M.; Poltorak, M.; Stemberger, C.; Schumann, K.; Roth, T.L.; Marson, A.; et al. Orthotopic replacement of T-cell receptor α- and β-chains with preservation of near-physiological T-cell function. Nat. Biomed. Eng. 2019, 3, 974–984. [Google Scholar] [CrossRef]
- Stadtmauer, E.A.; Fraietta, J.A.; Davis, M.M.; Cohen, A.D.; Weber, K.L.; Lancaster, E.; Mangan, P.A.; Kulikovskaya, I.; Gupta, M.; Chen, F.; et al. CRISPR-engineered T cells in patients with refractory cancer. Science 2020, 367, 6481. [Google Scholar] [CrossRef] [PubMed]
- Charlesworth, C.T.; Deshpande, P.S.; Dever, D.P.; Camarena, J.; Lemgart, V.T.; Cromer, M.K.; Vakulskas, C.A.; Collingwood, M.A.; Zhang, L.; Bode, N.M.; et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 2019, 25, 249–254. [Google Scholar] [CrossRef] [PubMed]
- Martins, F.; Sofiya, L.; Sykiotis, G.P.; Lamine, F.; Maillard, M.; Fraga, M.; Shabafrouz, K.; Ribi, C.; Cairoli, A.; Guex-Crosier, Y.; et al. Adverse effects of immune-checkpoint inhibitors: Epidemiology, management and surveillance. Nat. Rev. Clin. Oncol. 2019, 16, 563–580. [Google Scholar] [CrossRef] [PubMed]
- Rupp, L.J.; Schumann, K.; Roybal, K.T.; Gate, R.E.; Ye, C.J.; Lim, W.A.; Marson, A. CRISPR/Cas9-mediated PD-1 disruption enhances anti-Tumor efficacy of human chimeric antigen receptor T cells. Sci. Rep. 2017, 7, 737. [Google Scholar] [CrossRef]
- Wei, J.; Long, L.; Zheng, W.; Dhungana, Y.; Lim, S.A.; Guy, C.; Wang, Y.; Wang, Y.-D.; Qian, C.; Xu, B.; et al. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature 2019, 576, 471–476. [Google Scholar] [CrossRef]
- Singer, M.; Wang, C.; Cong, L.; Marjanovic, N.D.; Kowalczyk, M.S.; Zhang, H.; Nyman, J.; Sakuishi, K.; Kurtulus, S.; Gennert, D.; et al. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell 2016, 166, 1500–1511. [Google Scholar] [CrossRef]
- Campana, D.; Van Dongen, J.J.M.; Mehta, A.; Coustan-Smith, E.; Wolvers-Tettero, I.L.M.; Ganeshaguru, K.; Janossy, G. Stages of T-cell Receptor Protein Expression in T-cell Acute Lymphoblastic Leukemia. Blood 1991, 77, 1546–1554. [Google Scholar] [CrossRef] [Green Version]
- Jones, N.H.; Clabby, M.L.; Dialynas, D.P.; Huang, H.J.S.; Herzenberg, L.A.; Strominger, J.L. Isolation of complementary DNA clones encoding the human lymphocyte glycoprotein T1/Leu-1. Nature 1986, 323, 346–349. [Google Scholar] [CrossRef]
- Pui, C.-H.; Behm, F.G.; Crist, W.M. Clinical and Biologic Relevance of Immunologic Marker Studies in Childhood Acute Lymphoblastic Leukemia. Blood 1993, 82, 342–362. [Google Scholar] [CrossRef] [Green Version]
- Gomes-Silva, D.; Srinivasan, M.; Sharma, S.; Lee, C.M.; Wagner, D.L.; Davis, T.H.; Rouce, R.H.; Bao, G.; Brenner, M.K.; Mamonkin, M. CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies. Blood 2017, 130, 285–296. [Google Scholar] [CrossRef]
- Cooper, M.L.; Choi, J.; Staser, K.; Ritchey, J.K.; Devenport, J.M.; Eckardt, K.; Rettig, M.P.; Wang, B.; Eissenberg, L.G.; Ghobadi, A.; et al. An “off-the-shelf” fratricide-resistant CAR-T for the treatment of T cell hematologic malignancies. Leukemia 2018, 32, 1970–1983. [Google Scholar] [CrossRef] [PubMed]
- Mamonkin, M.; Rouce, R.H.; Tashiro, H.; Brenner, M.K. A T-cell-directed chimeric antigen receptor for the selective treatment of T-cell malignancies. Blood 2015, 126, 983–992. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Depil, S.; Duchateau, P.; Grupp, S.A.; Mufti, G.; Poirot, L. “Off-the-shelf” allogeneic CAR T cells: Development and challenges. Nat. Rev. Drug Discov. 2020, 19, 185–199. [Google Scholar] [CrossRef]
- Aversa, F.; Tabilio, A.; Velardi, A.; Cunningham, I.; Terenzi, A.; Falzetti, F.; Ruggeri, L.; Barbabietola, G.; Aristei, C.; Latini, P.; et al. Treatment of high-risk acute leukemia with T-cell-depleted stem cells from related donors with one fully mismatched HLA haplotype. N. Engl. J. Med. 1998, 339, 1186–1193. [Google Scholar] [CrossRef] [PubMed]
- Abdelhakim, H.; Abdel-Azim, H.; Saad, A. Role of αβ T Cell Depletion in Prevention of Graft versus Host Disease. Biomedicines 2017, 5. [Google Scholar] [CrossRef] [Green Version]
- Felix, N.J.; Allen, P.M. Specificity of T-cell alloreactivity. Nat. Rev. Immunol. 2007, 7, 942–953. [Google Scholar] [CrossRef]
- Wang, D.; Quan, Y.; Yan, Q.; Morales, J.E.; Wetsel, R.A. Targeted Disruption of the β2-Microglobulin Gene Minimizes the Immunogenicity of Human Embryonic Stem Cells. Stem Cells Transl. Med. 2015, 4, 1234–1245. [Google Scholar] [CrossRef]
- Xiao, Q.; Guo, D.; Chen, S. Application of CRISPR/Cas9-based gene editing in HIV-1/AIDS therapy. Front. Cell. Infect. Microbiol. 2019, 9, 69. [Google Scholar] [CrossRef]
- Chun, T.W.; Moir, S.; Fauci, A.S. HIV reservoirs as obstacles and opportunities for an HIV cure. Nat. Immunol. 2015, 16, 584–589. [Google Scholar] [CrossRef]
- Ebina, H.; Misawa, N.; Kanemura, Y.; Koyanagi, Y. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci. Rep. 2013, 3, 2510. [Google Scholar] [CrossRef] [Green Version]
- Hu, W.; Kaminski, R.; Yang, F.; Zhang, Y.; Cosentino, L.; Li, F.; Luo, B.; Alvarez-Carbonell, D.; Garcia-Mesa, Y.; Karn, J.; et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc. Natl. Acad. Sci. USA 2014, 111, 11461–11466. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kaminski, R.; Chen, Y.; Fischer, T.; Tedaldi, E.; Napoli, A.; Zhang, Y.; Karn, J.; Hu, W.; Khalili, K. Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing. Sci. Rep. 2016, 6. [Google Scholar] [CrossRef] [Green Version]
- Liao, H.K.; Gu, Y.; Diaz, A.; Marlett, J.; Takahashi, Y.; Li, M.; Suzuki, K.; Xu, R.; Hishida, T.; Chang, C.J.; et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat. Commun. 2015, 6, 7413. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kaminski, R.; Bella, R.; Yin, C.; Otte, J.; Ferrante, P.; Gendelman, H.E.; Li, H.; Booze, R.; Gordon, J.; Hu, W.; et al. Excision of HIV-1 DNA by gene editing: A proof-of-concept in vivo study. Gene Ther. 2016, 23, 690–695. [Google Scholar] [CrossRef] [PubMed]
- Yin, L.; Hu, S.; Mei, S.; Sun, H.; Xu, F.; Li, J.; Zhu, W.; Liu, X.; Zhao, F.; Zhang, D.; et al. CRISPR/Cas9 Inhibits Multiple Steps of HIV-1 Infection. Hum. Gene Ther. 2018, 29, 1264–1276. [Google Scholar] [CrossRef]
- Dash, P.K.; Kaminski, R.; Bella, R.; Su, H.; Mathews, S.; Ahooyi, T.M.; Chen, C.; Mancuso, P.; Sariyer, R.; Ferrante, P.; et al. Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice. Nat. Commun. 2019, 10, 2753. [Google Scholar] [CrossRef] [Green Version]
- Hütter, G.; Nowak, D.; Mossner, M.; Ganepola, S.; Müßig, A.; Allers, K.; Schneider, T.; Hofmann, J.; Kücherer, C.; Blau, O.; et al. Long-Term Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation. N. Engl. J. Med. 2009, 360, 692–698. [Google Scholar] [CrossRef] [Green Version]
- Tebas, P.; Stein, D.; Tang, W.W.; Frank, I.; Wang, S.Q.; Lee, G.; Spratt, S.K.; Surosky, R.T.; Giedlin, M.A.; Nichol, G.; et al. Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV. N. Engl. J. Med. 2014, 370, 901–910. [Google Scholar] [CrossRef] [Green Version]
- Qi, C.; Li, D.; Jiang, X.; Jia, X.; Lu, L.; Wang, Y.; Sun, J.; Shao, Y.; Wei, M. Inducing CCR5Δ32/Δ32 Homozygotes in the Human Jurkat CD4+ Cell Line and Primary CD4+ Cells by CRISPR-Cas9 Genome-Editing Technology. Mol. Ther. Nucleic Acids 2018, 12, 267–274. [Google Scholar] [CrossRef] [Green Version]
- Li, C.; Guan, X.; Du, T.; Jin, W.; Wu, B.; Liu, Y.; Wang, P.; Hu, B.; Griffin, G.E.; Shattock, R.J.; et al. Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J. Gen. Virol. 2015, 96, 2381–2393. [Google Scholar] [CrossRef]
- Hou, P.; Chen, S.; Wang, S.; Yu, X.; Chen, Y.; Jiang, M.; Zhuang, K.; Ho, W.; Hou, W.; Huang, J.; et al. Genome editing of CXCR4 by CRISPR/cas9 confers cells resistant to HIV-1 infection. Sci. Rep. 2015, 5, 15577. [Google Scholar] [CrossRef] [PubMed]
- Connor, R.I.; Sheridan, K.E.; Ceradini, D.; Choe, S.; Landau, N.R. Change in coreceptor use correlates with disease progression in HIV-1- infected individuals. J. Exp. Med. 1997, 185, 621–628. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, Z.; Chen, S.; Jin, X.; Wang, Q.; Yang, K.; Li, C.; Xiao, Q.; Hou, P.; Liu, S.; Wu, S.; et al. Genome editing of the HIV co-receptors CCR5 and CXCR4 by CRISPR-Cas9 protects CD4+ T cells from HIV-1 infection. Cell Biosci. 2017, 7, 47. [Google Scholar] [CrossRef] [PubMed]
- Yu, S.; Yao, Y.; Xiao, H.; Li, J.; Liu, Q.; Yang, Y.; Adah, D.; Lu, J.; Zhao, S.; Qin, L.; et al. Simultaneous Knockout of CXCR4 and CCR5 Genes in CD4+ T Cells via CRISPR/Cas9 Confers Resistance to Both X4- and R5-Tropic Human Immunodeficiency Virus Type 1 Infection. Hum. Gene Ther. 2018, 29, 51–67. [Google Scholar] [CrossRef]
- Wang, Q.; Chen, S.; Xiao, Q.; Liu, Z.; Liu, S.; Hou, P.; Zhou, L.; Hou, W.; Ho, W.; Li, C.; et al. Genome modification of CXCR4 by Staphylococcus aureus Cas9 renders cells resistance to HIV-1 infection. Retrovirology 2017, 14, 51. [Google Scholar] [CrossRef] [Green Version]
- Liu, Z.; Liang, J.; Chen, S.; Wang, K.; Liu, X.; Liu, B.; Xia, Y.; Guo, M.; Zhang, X.; Sun, G.; et al. Genome editing of CCR5 by AsCpf1 renders CD4+T cells resistance to HIV-1 infection. Cell Biosci. 2020, 10, 85. [Google Scholar] [CrossRef]
- Tian, S.; Choi, W.-T.; Liu, D.; Pesavento, J.; Wang, Y.; An, J.; Sodroski, J.G.; Huang, Z. Distinct Functional Sites for Human Immunodeficiency Virus Type 1 and Stromal Cell-Derived Factor 1α on CXCR4 Transmembrane Helical Domains. J. Virol. 2005, 79, 12667–12673. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- DiTommaso, T.; Cole, J.M.; Cassereau, L.; Buggé, J.A.; Sikora Hanson, J.L.; Bridgen, D.T.; Stokes, B.D.; Loughhead, S.M.; Beutel, B.A.; Gilbert, J.B.; et al. Cell engineering with microfluidic squeezing preserves functionality of primary immune cells in vivo. Proc. Natl. Acad. Sci. USA 2018, 115, E10907–E10914. [Google Scholar] [CrossRef] [Green Version]
- Anzalone, A.V.; Randolph, P.B.; Davis, J.R.; Sousa, A.A.; Koblan, L.W.; Levy, J.M.; Chen, P.J.; Wilson, C.; Newby, G.A.; Raguram, A.; et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 2019, 576, 149–157. [Google Scholar] [CrossRef]
- Liu, M.; Rehman, S.; Tang, X.; Gu, K.; Fan, Q.; Chen, D.; Ma, W. Methodologies for Improving HDR Efficiency. Front. Genet. 2018, 9, 691. [Google Scholar] [CrossRef]
- Liu, J.; Srinivasan, S.; Li, C.-Y.; Ho, I.-L.; Rose, J.; Shaheen, M.; Wang, G.; Yao, W.; Deem, A.; Bristow, C.; et al. Pooled library screening with multiplexed Cpf1 library. Nat. Commun. 2019, 10, 3144. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Mode of Delivery | ||||||||
---|---|---|---|---|---|---|---|---|
Electroporation | Viral | Endogenous | ||||||
RNP | mRNA | DNA | Lentivirus | Adenovirus | AAV | Cas9 mice | ||
Knockouts | Single gene | Seki and Rutz 2018 [16] Schumann et al. [20] Vakulskas et al. [23] Hendel et al. [27] Nüssing et al. [36] Shifrut et al. [65]Ye et al. [70] Rupp et al. [84] Gomes-Silva et al. [90] | Ren et al. [21] Hendel et al. [27] Gaudelli et al. [44] Gwiazda et al. [57] Cooper et al. [91] | Hendel et al. [27] Su et al. [30] Mandal et al. [31] Kornete et al. [48] Hou et al. [111] Liu et al. [113] | Legut et al. [79] Singer et al. [86] Kaminski et al. [102] Qi et al. [109] | Li et al. [110] Liu et al. [116] | Wang et al. [115] | LaFleur et al. [34] Chu et al. [35] Dong et al. [69] Ye et al. [70] |
Multiplexed | Webber et al. [26] Nüssing et al. [36] Stadtmauer et al. [81] Yu et al. [114] | Ren et al. [21] Webber et al. [26] Ren et al. [41] Gaudelli et al. [44] Gwiazda et al. [57] | Liu et al. [40] Kornete et al. [48] Liu et al. [113] | |||||
Pooled | Shifrut et al. [65] Ting et al. [68] | LaFleur et al. [34] Dong et al. [69] Ye et al. [70] Henriksson et al. [71] Cortez et al. [72] Wei et al. [85] | ||||||
Knockins | Single gene | Schumann et al. [20] Vakulskas 2018 [23] Roth et al. [29] Nüssing et al. [36] Nguyen et al. [56] Wienert et al. [61] Schober et al. [80] | Eyquem et al. [28] Gwiazda et al. [57] | Kornete et al. [48] | ||||
Mutliplexed | Roth et al. [29] Nguyen et al. [56] Schober et al. [80] | Dai et al. [38] | Kornete et al. [48] | |||||
Pooled | Roth et al. [73] |
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Kotowski, M.; Sharma, S. CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells. Methods Protoc. 2020, 3, 79. https://doi.org/10.3390/mps3040079
Kotowski M, Sharma S. CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells. Methods and Protocols. 2020; 3(4):79. https://doi.org/10.3390/mps3040079
Chicago/Turabian StyleKotowski, Mateusz, and Sumana Sharma. 2020. "CRISPR-Based Editing Techniques for Genetic Manipulation of Primary T Cells" Methods and Protocols 3, no. 4: 79. https://doi.org/10.3390/mps3040079