New Bicistronic TALENs Greatly Improve Genome Editing
José María Martín-Fernández
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Search for more papers by this authorAarne Fleischer
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorSara Vallejo-Diez
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorEsther Palomino
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorAlmudena Sánchez-Gilabert
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorRaúl Ruiz
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorYazmine Bejarano
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Current address: Centro de Investigación del Cáncer, Campus Miguel de Unamuno, Salamanca, Spain
Search for more papers by this authorPere Llinàs
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Current address: Josep Carreras Leukaemia Research Institute (IJC), Ctra. de Can Ruti, Camí de les Escoles, Badalona, Spain
Search for more papers by this authorAntoni Gayá
Instituto de Investigación Sanitaria Illes Balears (IDISBA), Fundació Banc de Sang i Teixits de les Illes Balears (FBSTIB), Grupo de Terapia Celular e Ingenieria Tisular, Palma de Mallorca, Spain
Search for more papers by this authorCorresponding Author
Daniel Bachiller
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Corresponding author: [email protected]Search for more papers by this authorJosé María Martín-Fernández
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Search for more papers by this authorAarne Fleischer
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorSara Vallejo-Diez
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorEsther Palomino
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorAlmudena Sánchez-Gilabert
Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorRaúl Ruiz
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Search for more papers by this authorYazmine Bejarano
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Current address: Centro de Investigación del Cáncer, Campus Miguel de Unamuno, Salamanca, Spain
Search for more papers by this authorPere Llinàs
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Current address: Josep Carreras Leukaemia Research Institute (IJC), Ctra. de Can Ruti, Camí de les Escoles, Badalona, Spain
Search for more papers by this authorAntoni Gayá
Instituto de Investigación Sanitaria Illes Balears (IDISBA), Fundació Banc de Sang i Teixits de les Illes Balears (FBSTIB), Grupo de Terapia Celular e Ingenieria Tisular, Palma de Mallorca, Spain
Search for more papers by this authorCorresponding Author
Daniel Bachiller
Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
Corresponding author: [email protected]Search for more papers by this authorAbstract
Genome editing has become one of the most powerful tools in present-day stem cell and regenerative medicine research, but despite its rapid acceptance and widespread use, some elements of the technology still need improvement. In this unit, we present data regarding the use of a new, more efficient type of transcription activator-like effector nuclease (TALEN) for gene editing. Our group has generated bicistronic genes in which classical TALEN coding sequences are linked by 2A elements to different reporter molecules, such as fluorochromes (TALEN-F) or membrane receptors (TALEN-M). This structure results in two proteins transcribed from the same transcript, of which the second (the reporter) can be used as the target for selection by fluorescence-assisted cell sorting (FACS) or magnetic-activated cell sorting (MACS). The application of these new TALEN genes allows a rapid enrichment of cells in which both members of the TALEN pair are active, thus eliminating the need for lengthy selection in culture and laborious characterization of a large number of clones. © 2020 by John Wiley & Sons, Inc.
Basic Protocol 1: Generation of new TALENs
Basic Protocol 2: Genome editing using TALEN-F
Alternate Protocol 1: Generation of TALEN-M
Support Protocol 1: mRNA in vitro transcription (IVT) of TALEN-T2A-reporter expression vector
Alternate Protocol 2: Editing of primary T cells using TALEN-M
Basic Protocol 3: Verifying gene editing
Support Protocol 2: Rapid expansion protocol for edited T-cells
Literature Cited
- Aihara, M., Dobashi, K., Iizuka, K., Nakazawa, T., & Mori, M. (2003). Comparison of effects of Y-27632 and isoproterenol on release of cytokines from human peripheral T cells. International Immunopharmacology, 3(12), 1619–1625. doi: 10.1016/S1567-5769(03)00184-X.
- Alexopoulou, L., Holt, A. C., Medzhitov, R., & Flavell, R. A. (2001). Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature, 413(6857), 732–738. doi: 10.1038/35099560.
- Bachiller, D. (2018). Treating AIDs with TALENs. Paper presented at the 9th Biennial Congress. Spanish Society of Gene and Cell Therapy: Cell and Gene Immunotherapy, Palma de Mallorca.
- Bachiller, D., Martin-Fernandez, J. M., Vallejo, S., Sanchez, A., Castresana, M., & Fleischer, A. (2019). New Polycistronic TALENs greatly improve genome editing. Paper presented at the LA 20019 International Society for Stem Cell Research annual meeting: Technologies for Stem Cell Research.
- Biddison, W. E. (2001). Preparation and culture of human lymphocytes. Current Protocols in Cell Biology, 00(1), 2.2.1–2.2.13. doi: 10.1002/0471143030.cb0202s00.
- Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., & Bonas, U. (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science, 326(5959), 1509–1512. doi: 10.1126/science.1178811.
- Bogdanove, A. J., Schornack, S., & Lahaye, T. (2010). TAL effectors: Finding plant genes for disease and defense. Current Opinion in Plant Biology, 13(4), 394–401. doi: 10.1016/j.pbi.2010.04.010S1369-5266(10)00053-1.
- Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., & Voytas, D. F. (2011). Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research, 39(12), e82. doi: 10.1093/nar/gkr218.
- Chiang, C., Beljanski, V., Yin, K., Olagnier, D., Ben Yebdri, F., Steel, C., & Hiscott, J. (2015). Sequence-specific modifications enhance the broad-spectrum antiviral response activated by RIG-I agonists. Journal of Virology, 89(15), 8011–8025. doi: 10.1128/JVI.00845-15.
- Deng, D., Yan, C., Pan, X., Mahfouz, M., Wang, J., Zhu, J. K., & Yan, N. (2012). Structural basis for sequence-specific recognition of DNA by TAL effectors. Science, 335(6069), 720–723. doi: 10.1126/science.1215670.
- Devine, S. M., Carter, S., Soiffer, R. J., Pasquini, M. C., Hari, P. N., Stein, A., & O'Reilly, R. J. (2011). Low risk of chronic graft-versus-host disease and relapse associated with T cell-depleted peripheral blood stem cell transplantation for acute myelogenous leukemia in first remission: Results of the blood and marrow transplant clinical trials network protocol 0303. Biology of Blood and Marrow Transplantation, 17(9), 1343–1351. doi: 10.1016/j.bbmt.2011.02.002S1083-8791(11)00096-6.
- Donnelly, M. L., Luke, G., Mehrotra, A., Li, X., Hughes, L. E., Gani, D., & Ryan, M. D. (2001). Analysis of the aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: A putative ribosomal ‘skip’. Journal of General Virology, 82(Pt 5), 1013–1025. doi: 10.1099/0022-1317-82-5-1013.
- Dudley, M. E., Wunderlich, J. R., Shelton, T. E., Even, J., & Rosenberg, S. A. (2003). Generation of tumor-infiltrating lymphocyte cultures for use in adoptive transfer therapy for melanoma patients. Journal of Immunotherapy, 26(4), 332–342.
- Feng, Q., Hato, S. V., Langereis, M. A., Zoll, J., Virgen-Slane, R., Peisley, A., & van Kuppeveld, F. J. (2012). MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells. Cell Reports, 2(5), 1187–1196. doi: 10.1016/j.celrep.2012.10.005S2211-1247(12)00341-5.
- Fleischer, A. (2018). TALEN-mediated correction of p.F508del and restoration of CFTR function in hiPS-derived intestinal organoids. Paper presented at the 9th Biennial Congress of the Spanish Society of Gene and Cell Therapy: Organoids and Gene Transfer Models, Palma de Mallorca.
- Fleischer, A., Palomino, E., Martin-Fernandez, J. M., Castresana, M., Vallejo, S., & Bachiller, D. (2017). Correction and functional characterisation of the p.F508del cystic fibrosis mutation in patient-derived iPS cells. Paper presented at the ESGCT XXV Anniversary Congress, Berlin.
- Gainza Lafuente, E. J., Gainza Lucea, G., Del Pozo Perez, A., Pastor Navarro, M., Pedraz Muñoz, J. L., Viñas Ciordia, M., … Galvez Jerez, V. (2016). World Patent no. WO2016203088.
- Gaj, T., Gersbach, C. A., & Barbas, C. F., 3rd (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397–405. doi: 10.1016/j.tibtech.2013.04.004S0167-7799(13)00087-5.
- Gonzalez, F., Zhu, Z., Shi, Z. D., Lelli, K., Verma, N., Li, Q. V., & Huangfu, D. (2014). An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells. Cell Stem Cell, 15(2), 215–226. doi: 10.1016/j.stem.2014.05.018.
- Goswami, R., Subramanian, G., Silayeva, L., Newkirk, I., Doctor, D., Chawla, K., & Betapudi, V. (2019). Gene therapy leaves a vicious cycle. Frontiers in Oncology, 9, 297. doi: 10.3389/fonc.2019.00297.
- Goubau, D., Schlee, M., Deddouche, S., Pruijssers, A. J., Zillinger, T., Goldeck, M., & Reis e Sousa, C. (2014). Antiviral immunity via RIG-I-mediated recognition of RNA bearing 5′-diphosphates. Nature, 514(7522), 372–375. doi: 10.1038/nature13590.
- Hasan, Z., Palani, K., Zhang, S., Lepsenyi, M., Hwaiz, R., Rahman, M., & Thorlacius, H. (2013). Rho kinase regulates induction of T-cell immune dysfunction in abdominal sepsis. Infection and Immunity, 81(7), 2499–2506. doi: 10.1128/IAI.00126-13IAI.00126-13.
- Heil, F., Hemmi, H., Hochrein, H., Ampenberger, F., Kirschning, C., Akira, S., & Bauer, S. (2004). Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science, 303(5663), 1526–1529. doi: 10.1126/science.1093620.
- Hornung, V., Ellegast, J., Kim, S., Brzozka, K., Jung, A., Kato, H., & Hartmann, G. (2006). 5′-Triphosphate RNA is the ligand for RIG-I. Science, 314(5801), 994–997. doi: 10.1126/science.1132505.
- Hull, C. M., & Bevilacqua, P. C. (2016). Discriminating self and non-self by RNA: Roles for RNA structure, misfolding, and modification in regulating the innate immune sensor PKR. Accounts of Chemical Research, 49(6), 1242–1249. doi: 10.1021/acs.accounts.6b00151.
- Jang, Y. Y., & Ye, Z. (2016). Gene correction in patient-specific iPSCs for therapy development and disease modeling. Human Genetics, 135(9), 1041–1058. doi: 10.1007/s00439-016-1691-5.
- Kim, H., & Kim, J. S. (2014). A guide to genome engineering with programmable nucleases. Nature Reviews Genetics, 15(5), 321–334. doi: 10.1038/nrg3686.
- Kim, S. I., Matsumoto, T., Kagawa, H., Nakamura, M., Hirohata, R., Ueno, A., & Woltjen, K. (2018). Microhomology-assisted scarless genome editing in human iPSCs. Nature Communications, 9(1), 939. doi: 10.1038/s41467-018-03044-y.
- Kumar, P., Sweeney, T. R., Skabkin, M. A., Skabkina, O. V., Hellen, C. U., & Pestova, T. V. (2014). Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp-mRNAs. Nucleic Acids Research, 42(5), 3228–3245. doi: 10.1093/nar/gkt1321.
- Kwart, D., Paquet, D., Teo, S., & Tessier-Lavigne, M. (2017). Precise and efficient scarless genome editing in stem cells using CORRECT. Nature Protocols, 12(2), 329–354. doi: 10.1038/nprot.2016.171.
- Lambricht, L., Lopes, A., Kos, S., Sersa, G., Preat, V., & Vandermeulen, G. (2016). Clinical potential of electroporation for gene therapy and DNA vaccine delivery. Expert Opinion on Drug Delivery, 13(2), 295–310. doi: 10.1517/17425247.2016.1121990.
- Li, L., & Peshwa, M. V. (2017). US Patent o. US9669058B2.
- Lou, Z., Billadeau, D. D., Savoy, D. N., Schoon, R. A., & Leibson, P. J. (2001). A role for a RhoA/ROCK/LIM-kinase pathway in the regulation of cytotoxic lymphocytes. Journal of Immunology, 167(10), 5749–5757. doi: 10.4049/jimmunol.167.10.5749.
- Mak, A. N., Bradley, P., Cernadas, R. A., Bogdanove, A. J., & Stoddard, B. L. (2012). The crystal structure of TAL effector PthXo1 bound to its DNA target. Science, 335(6069), 716–719. doi: 10.1126/science.1216211.
- Mangeot, P. E., Risson, V., Fusil, F., Marnef, A., Laurent, E., Blin, J., & Ricci, E. P. (2019). Genome editing in primary cells and in vivo using viral-derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins. Nature Communications, 10(1), 45. doi: 10.1038/s41467-018-07845-z.
- Martin-Fernandez, J. M, Vallejo, S., Salgado, M., Galvez, C., Martin, V., Fleischer, A., … Bachiller, D. (2017). Nuevas herramientas de Ingeniería Genómica para el tratamiento del SIDA. Paper presented at the Spanish Society of Infectious Diseases and Clinical Microbiology: Inmunologia de la infección por VIH y Vacunas, Vigo.
- Moscou, M. J., & Bogdanove, A. J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science, 326(5959), 1501. doi: 10.1126/science.1178817.
- Nagasaki, A., Kato, Y., Meguro, K., Yamagishi, A., Nakamura, C., & Uyeda, T. Q. P. (2018). A genome editing vector that enables easy selection and identification of knockout cells. Plasmid, 98, 37–44. doi: 1016/j.plasmid.2018.08.005.
- Paquet, D., Kwart, D., Chen, A., Sproul, A., Jacob, S., Teo, S., & Tessier-Lavigne, M. (2016). Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9. Nature, 533(7601), 125–129. doi: 10.1038/nature17664.
- Park, A., Hong, P., Won, S. T., Thibault, P. A., Vigant, F., Oguntuyo, K. Y., & Lee, B. (2016). Sendai virus, an RNA virus with no risk of genomic integration, delivers CRISPR/Cas9 for efficient gene editing. Molecular Therapy: Methods & Clinical Development, 3, 16057. doi: 10.1038/mtm.2016.57.
- Pichlmair, A., Schulz, O., Tan, C. P., Naslund, T. I., Liljestrom, P., Weber, F., & Reis e Sousa, C. (2006). RIG-I-mediated antiviral responses to single-stranded RNA bearing 5′-phosphates. Science, 314(5801), 997–1001. doi: 10.1126/science.1132998.
- Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013). Genome engineering using the CRISPR-Cas9 system. Nature Protocols, 8(11), 2281–2308. doi: 10.1038/nprot.2013.143.
- Reyon, D., Tsai, S. Q., Khayter, C., Foden, J. A., Sander, J. D., & Joung, J. K. (2012). FLASH assembly of TALENs for high-throughput genome editing. Nature Biotechnology, 30(5), 460–465. doi: 10.1038/nbt.2170.
- Saha, S. K., Saikot, F. K., Rahman, M. S., Jamal, M., Rahman, S. M. K., Islam, S. M. R., & Kim, K. H. (2019). Programmable molecular scissors: Applications of a new tool for genome editing in biotech. Molecular Therapy: Nucleic Acids, 14, 212–238. doi: 10.1016/j.omtn.2018.11.016.
- Schlee, M., Roth, A., Hornung, V., Hagmann, C. A., Wimmenauer, V., Barchet, W., & Hartmann, G. (2009). Recognition of 5′ triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity, 31(1), 25–34. doi: 10.1016/j.immuni.2009.05.008S1074-7613(09)00271-4.
- Supharattanasitthi, W., Carlsson, E., Sharif, U., & Paraoan, L. (2019). CRISPR/Cas9-mediated one step bi-allelic change of genomic DNA in iPSCs and human RPE cells in vitro with dual antibiotic selection. Scientific Reports, 9(1), 174. doi: 10.1038/s41598-018-36740-2.
- Sutermaster, B. A., & Darling, E. M. (2019). Considerations for high-yield, high-throughput cell enrichment: Fluorescence versus magnetic sorting. Scientific Reports, 9(1), 227. doi: 10.1038/s41598-018-36698-1.
- Tharaux, P. L., Bukoski, R. C., Rocha, P. N., Crowley, S. D., Ruiz, P., Nataraj, C., & Coffman, T. M. (2003). Rho kinase promotes alloimmune responses by regulating the proliferation and structure of T cells. Journal of Immunology, 171(1), 96–105. doi: 10.4049/jimmunol.171.1.96.
- Uzri, D., & Gehrke, L. (2009). Nucleotide sequences and modifications that determine RIG-I/RNA binding and signaling activities. Journal of Virology, 83(9), 4174–4184. doi: 10.1128/JVI.02449-08.
- Vaidyanathan, S., Azizian, K. T., Haque, A., Henderson, J. M., Hendel, A., Shore, S., … McCaffrey, A. P. (2018). Uridine depletion and chemical modification increase Cas9 mRNA activity and reduce immunogenicity without HPLC purification. Molecular Therapy: Nucleic Acids, 12, 530–542. doi: 1016/j.omtn.2018.06.010.
- Weber, M., & Weber, F. (2014). Segmented negative-strand RNA viruses and RIG-I: Divide (your genome) and rule. Current Opinion in Microbiology, 20, 96–102. doi: 10.1016/j.mib.2014.05.002S1369-5274(14)00049-6.
- Yang, J. Q., Kalim, K. W., Li, Y., Zhang, S., Hinge, A., Filippi, M. D., & Guo, F. (2016). RhoA orchestrates glycolysis for TH2 cell differentiation and allergic airway inflammation. Journal of Allergy and Clinical Immunology, 137(1), 231–245.e4. doi: 1016/j.jaci.2015.05.004.