Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Empowering gene delivery with protein engineering platforms

Abstract

The repertoire of therapeutic proteins has been substantially augmented by molecular engineering approaches, which have seen remarkable advancement in recent years. In particular, advances in directed evolution technologies have empowered the development of custom-designed proteins with novel and disease-relevant functions. Whereas engineered proteins have typically been administered through systemic injection of the purified molecule, exciting progress in gene delivery affords the opportunity to elicit sustained production of the engineered proteins by targeted cells in the host organism. Combining developments at the leading edge of protein engineering and gene delivery has catapulted a new wave of molecular and cellular therapy approaches, which harbor great promise for personalized and precision medicine. This mini-review outlines currently used display platforms for protein evolution and describes recent examples of how the resulting engineered proteins have been incorporated into DNA- and cell-based therapeutic platforms, both in vitro and in vivo. Collectively, the strategies detailed herein provide a framework for synthesizing molecular engineering workflows with gene therapy systems for a breadth of applications in research and medicine.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Schematic representations of protein display systems.
Fig. 2: Gene delivery of engineered proteins.
Fig. 3: Advances in Chimeric Antigen Receptor (CAR) engineering.

Similar content being viewed by others

Data availability

Data sharing is not applicable to this paper as no datasets were generated or analyzed during the current study.

References

  1. Ryu DDY, Nam D-H. Recent Progress in Biomolecular Engineering. Biotechnol Prog. 2000;16:2–16.

    Article  PubMed  CAS  Google Scholar 

  2. Mahdavi SZB, Oroojalian F, Eyvazi S, Hejazi M, Baradaran B, Pouladi N, et al. An overview on display systems (phage, bacterial, and yeast display) for production of anticancer antibodies; advantages and disadvantages. Int J Biol Macromol. 2022;208:421–42.

    Article  PubMed  CAS  Google Scholar 

  3. Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 1985;228:1315–7.

    Article  PubMed  CAS  Google Scholar 

  4. Lee CV, Sidhu SS, Fuh G. Bivalent antibody phage display mimics natural immunoglobulin. J Immunol Methods. 2004;284:119–32.

    Article  PubMed  CAS  Google Scholar 

  5. Ledsgaard L, Kilstrup M, Karatt-Vellatt A, McCafferty J, Laustsen AH. Basics of antibody phage display technology. Toxins 2018;10. https://doi.org/10.3390/toxins10060236.

  6. Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, et al. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol. 2020;11:1986.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Chasteen L, Ayriss J, Pavlik P, Bradbury ARM. Eliminating helper phage from phage display. Nucleic Acids Res. 2006;34:e145.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Hess GT, Cragnolini JJ, Popp MW, Allen MA, Dougan SK, Spooner E, et al. An M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins. Bioconjug Chem. 2012;23:1478–87.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Cherf GM, Cochran JR. Applications of yeast surface display for protein engineering. Methods Mol Biol (Clifton, NJ). 2015;1319:155.

    Article  Google Scholar 

  10. Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol. 1997;15:553–7.

    Article  PubMed  CAS  Google Scholar 

  11. Boder ET, Wittrup KD. Yeast surface display for directed evolution of protein expression, affinity, and stability. Methods Enzymol. 2000;328:430–44.

    Article  PubMed  CAS  Google Scholar 

  12. Chao G, Lau WL, Hackel BJ, Sazinsky SL, Lippow SM, Wittrup KD. Isolating and engineering human antibodies using yeast surface display. Nat Protoc. 2006;1:755–68.

    Article  PubMed  CAS  Google Scholar 

  13. Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J et al. Antibody display technologies: Selecting the cream of the crop. Biol Chem. 2021. https://doi.org/10.1515/HSZ-2020-0377/ASSET/GRAPHIC/J_HSZ-2020-0377_FIG_005.JPG.

  14. Tsuruta LR, dos ML, Moro AM. Display Technologies for the Selection of Monoclonal Antibodies for Clinical Use. Antibody Eng. 2017. https://doi.org/10.5772/INTECHOPEN.70930.

  15. Zhou C, Jacobsen FW, Cai L, Chen Q, Shen WD. Development of a novel mammalian cell surface antibody display platform. mAbs. 2010;2:508.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Bowers PM, Horlick RA, Kehry MR, Neben TY, Tomlinson GL, Altobell L, et al. Mammalian cell display for the discovery and optimization of antibody therapeutics. Methods. 2014;65:44–56.

    Article  PubMed  CAS  Google Scholar 

  17. Parthiban K, Perera RL, Sattar M, Huang Y, Mayle S, Masters E, et al. A comprehensive search of functional sequence space using large mammalian display libraries created by gene editing. mAbs. 2019;11:884–98.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Kanamori T, Fujino Y, Ueda T. PURE ribosome display and its application in antibody technology. Biochim et Biophys Acta - Proteins Proteom. 2014;1844:1925–32.

    Article  CAS  Google Scholar 

  19. He M. Ribosome display: Cell-free protein display technology. Briefings Funct Genom Proteom. 2002;1:204–12.

    Article  CAS  Google Scholar 

  20. Kunamneni A, Ogaugwu C, Bradfute S, Durvasula R. Ribosome Display Technology: Applications in Disease Diagnosis and Control. Antibodies. 2020;9:28.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Sockolosky JT, Trotta E, Parisi G, Picton L, Su LL, Le AC, et al. Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes. Science. 2018;359:1037–42.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Sedic M, Senn JJ, Lynn A, Laska M, Smith M, Platz SJ, et al. Safety Evaluation of Lipid Nanoparticle–Formulated Modified mRNA in the Sprague-Dawley Rat and Cynomolgus Monkey. Vet Pathol. 2018;55:341–54.

    Article  PubMed  CAS  Google Scholar 

  23. Haque AA, Dewerth A, Antony JS, Riethmüller J, Latifi N, Yasar H, et al. Modified hCFTR mRNA restores normal lung function in a mouse model of cystic fibrosis. 2017:202853. https://doi.org/10.1101/202853.

  24. Lou B, De Koker S, Lau CYJ, Hennink WE, Mastrobattista E. mRNA Polyplexes with Post-Conjugated GALA Peptides Efficiently Target, Transfect, and Activate Antigen Presenting Cells. Bioconjugate Chem. 2019;30:461–75.

    Article  CAS  Google Scholar 

  25. Kowalski PS, Rudra A, Miao L, Anderson DG. Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery. Mol Ther. 2019;27:710–28.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Nault J-C, Datta S, Imbeaud S, Franconi A, Mallet M, Couchy G, et al. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas. Nat Genet. 2015;47:1187–93.

    Article  PubMed  CAS  Google Scholar 

  27. Saunders KO, Wang L, Joyce MG, Yang Z-Y, Balazs AB, Cheng C, et al. Broadly Neutralizing Human Immunodeficiency Virus Type 1 Antibody Gene Transfer Protects Nonhuman Primates from Mucosal Simian-Human Immunodeficiency Virus Infection. J Virol. 2015;89:8334–45.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Sahay G, Querbes W, Alabi C, Eltoukhy A, Sarkar S, Zurenko C, et al. Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling. Nat Biotechnol. 2013;31:653–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Pardi N, Secreto AJ, Shan X, Debonera F, Glover J, Yi Y, et al. Administration of nucleoside-modified mRNA encoding broadly neutralizing antibody protects humanized mice from HIV-1 challenge. Nat Commun. 2017;8:14630.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Stadler CR, Bähr-Mahmud H, Celik L, Hebich B, Roth AS, Roth RP, et al. Elimination of large tumors in mice by mRNA-encoded bispecific antibodies. Nat Med. 2017;23:815–7.

    Article  PubMed  CAS  Google Scholar 

  31. Yin H, Kanasty RL, Eltoukhy AA, Vegas AJ, Dorkin JR, Anderson DG. Non-viral vectors for gene-based therapy. Nat Rev Genet. 2014;15:541–55.

    Article  PubMed  CAS  Google Scholar 

  32. Mukalel AJ, Riley RS, Zhang R, Mitchell MJ. Nanoparticles for nucleic acid delivery: Applications in cancer immunotherapy. Cancer Lett. 2019;458:102–12.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Malek TR, Yu A, Zhu L, Matsutani T, Adeegbe D, Bayer AL. IL-2 Family of Cytokines in T Regulatory Cell Development and Homeostasis. J Clin Immunol. 2008;28:635–9.

    Article  PubMed  CAS  Google Scholar 

  34. Létourneau S, Krieg C, Pantaleo G, Boyman O. IL-2– and CD25-dependent immunoregulatory mechanisms in the homeostasis of T-cell subsets. J Allergy Clin Immunol. 2009;123:758–62.

    Article  PubMed  Google Scholar 

  35. Zhang Q, Hresko ME, Picton LK, Su L, Hollander MJ, Nunez-Cruz S, et al. A human orthogonal IL-2 and IL-2Rβ system enhances CAR T cell expansion and antitumor activity in a murine model of leukemia. Sci Transl Med. 2021;13:eabg6986.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Hirai T, Ramos TL, Lin P-Y, Simonetta F, Su LL, Picton LK et al. Selective expansion of regulatory T cells using an orthogonal IL-2/IL-2 receptor system facilitates transplantation tolerance. 2021. https://doi.org/10.1172/JCI139991.

  37. Papadopoulos N, Martin J, Ruan Q, Rafique A, Rosconi MP, Shi E, et al. Binding and neutralization of vascular endothelial growth factor (VEGF) and related ligands by VEGF Trap, ranibizumab and bevacizumab. Angiogenesis. 2012;15:171–85.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Kureshi R, Zhu A, Shen J, Tzeng SY, Astrab LR, Sargunas PR, et al. Structure-Guided Molecular Engineering of a Vascular Endothelial Growth Factor Antagonist to Treat Retinal Diseases. Cel Mol Bioeng. 2020;13:405–18.

    Article  CAS  Google Scholar 

  39. June CH, O’Connor RS, Kawalekar OU, Ghassemi S, Milone MC. CAR T cell immunotherapy for human cancer. Science. 2018;359:1361–5.

    Article  PubMed  CAS  Google Scholar 

  40. Zajc CU, Salzer B, Taft JM, Reddy ST, Lehner M, Traxlmayr MW. Driving CARs with alternative navigation tools – the potential of engineered binding scaffolds. FEBS J. 2021;288:2103–18.

    Article  PubMed  CAS  Google Scholar 

  41. Subklewe M, von Bergwelt-Baildon M, Humpe A. Chimeric Antigen Receptor T Cells: A Race to Revolutionize Cancer Therapy. Transfus Med Hemother. 2019;46:15–24.

    Article  PubMed  PubMed Central  Google Scholar 

  42. Goodman DB, Azimi CS, Kearns K, Garakani K, Garcia J, Patel N et al. Pooled screening of CAR T cells identifies non-native signaling domains for next-generation immunotherapies. Immunology. 2021 https://doi.org/10.1101/2021.07.11.451980.

  43. Lanitis E, Rota G, Kosti P, Ronet C, Spill A, Seijo B, et al. Optimized gene engineering of murine CAR-T cells reveals the beneficial effects of IL-15 coexpression. J Exp Med. 2021;218:e20192203.

    Article  PubMed  CAS  Google Scholar 

  44. Zimmermann K, Kuehle J, Dragon AC, Galla M, Kloth C, Rudek LS, et al. Design and Characterization of an “All-in-One” Lentiviral Vector System Combining Constitutive Anti-GD2 CAR Expression and Inducible Cytokines. Cancers. 2020;12:375.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Chmielewski M, Abken H. CAR T Cells Releasing IL-18 Convert to T-Bethigh FoxO1low Effectors that Exhibit Augmented Activity against Advanced Solid Tumors. Cell Rep. 2017;21:3205–19.

    Article  PubMed  CAS  Google Scholar 

  46. Hu B, Ren J, Luo Y, Keith B, Young RM, Scholler J, et al. Augmentation of Antitumor Immunity by Human and Mouse CAR T Cells Secreting IL-18. Cell Rep. 2017;20:3025–33.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Krenciute G, Prinzing BL, Yi Z, Wu M-F, Liu H, Dotti G, et al. Transgenic Expression of IL15 Improves Antiglioma Activity of IL13Rα2-CAR T Cells but Results in Antigen Loss Variants. Cancer Immunol Res. 2017;5:571–81.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Ataca Atilla P, McKenna MK, Tashiro H, Srinivasan M, Mo F, Watanabe N, et al. Modulating TNFα activity allows transgenic IL15-Expressing CLL-1 CAR T cells to safely eliminate acute myeloid leukemia. J Immunother Cancer. 2020;8:e001229.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Gardner TJ, Lee JP, Bourne CM, Wijewarnasuriya D, Kinarivala N, Kurtz KG, et al. Engineering CAR-T cells to activate small-molecule drugs in situ. Nat Chem Biol. 2022;18:216–25.

    Article  PubMed  CAS  Google Scholar 

  50. Bouchkouj N, Kasamon YL, de Claro RA, George B, Lin X, Lee S, et al. FDA Approval Summary: Axicabtagene Ciloleucel for Relapsed or Refractory Large B-cell Lymphoma. Clinical Cancer Res. 2019;25:1702–8.

    Article  Google Scholar 

  51. O’Leary MC, Lu X, Huang Y, Lin X, Mahmood I, Przepiorka D, et al. FDA Approval Summary: Tisagenlecleucel for Treatment of Patients with Relapsed or Refractory B-cell Precursor Acute Lymphoblastic Leukemia. Clin Cancer Res. 2019;25:1142–6.

    Article  PubMed  Google Scholar 

  52. Lu T, Ma R, Dong W, Teng K-Y, Kollath DS, Li Z, et al. Off-the-shelf CAR natural killer cells secreting IL-15 target spike in treating COVID-19. Nat Commun. 2022;13:2576.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  53. Christodoulou I, Ho WJ, Marple A, Ravich JW, Tam A, Rahnama R, et al. Engineering CAR-NK cells to secrete IL-15 sustains their anti-AML functionality but is associated with systemic toxicities. J Immunother Cancer. 2021;9:e003894.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Daher M, Basar R, Gokdemir E, Baran N, Uprety N, Nunez Cortes AK, et al. Targeting a cytokine checkpoint enhances the fitness of armored cord blood CAR-NK cells. Blood. 2021;137:624–36.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Klichinsky M, Ruella M, Shestova O, Lu XM, Best A, Zeeman M, et al. Human chimeric antigen receptor macrophages for cancer immunotherapy. Nat Biotechnol. 2020;38:947–53.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Zmievskaya E, Valiullina A, Ganeeva I, Petukhov A, Rizvanov A, Bulatov E. Application of CAR-T Cell Therapy beyond Oncology: Autoimmune Diseases and Viral Infections. Biomedicines. 2021;9:59.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Marofi F, Motavalli R, Safonov VA, Thangavelu L, Yumashev AV, Alexander M, et al. CAR T cells in solid tumors: challenges and opportunities. Stem Cell Res Ther. 2021;12:81.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  58. Zhou T, Damsky W, Weizman O-E, McGeary MK, Hartmann KP, Rosen CE, et al. IL-18BP is a secreted immune checkpoint and barrier to IL-18 immunotherapy. Nature. 2020;583:609–14.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. Aronovich EL, McIvor RS, Hackett PB. The Sleeping Beauty transposon system: a non-viral vector for gene therapy. Human Mol Genet. 2011;20:R14–R20.

    Article  CAS  Google Scholar 

  60. Hurton LV, Singh H, Najjar AM, Switzer KC, Mi T, Maiti S et al. Tethered IL-15 augments antitumor activity and promotes a stem-cell memory subset in tumor-specific T cells. Proc Natl Acad Sci USA. 2016; 113. https://doi.org/10.1073/pnas.1610544113.

  61. Tugues S, Burkhard SH, Ohs I, Vrohlings M, Nussbaum K, vom Berg J, et al. New insights into IL-12-mediated tumor suppression. Cell Death Differ. 2015;22:237–46.

    Article  PubMed  CAS  Google Scholar 

  62. Shum T, Omer B, Tashiro H, Kruse RL, Wagner DL, Parikh K, et al. Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells. Cancer Discov. 2017;7:1238–47.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Huckaby JT, Landoni E, Jacobs TM, Savoldo B, Dotti G, Lai SK. Bispecific binder redirected lentiviral vector enables in vivo engineering of CAR-T cells. J Immunother Cancer. 2021;9:e002737.

    Article  PubMed  PubMed Central  Google Scholar 

  64. Nawaz W, Huang B, Xu S, Li Y, Zhu L, Yiqiao H, et al. AAV-mediated in vivo CAR gene therapy for targeting human T-cell leukemia. Blood Cancer J. 2021;11:119.

    Article  PubMed  PubMed Central  Google Scholar 

  65. Parayath NN, Stephan SB, Koehne AL, Nelson PS, Stephan MT. In vitro-transcribed antigen receptor mRNA nanocarriers for transient expression in circulating T cells in vivo. Nat Commun. 2020;11:6080.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Smith TT, Stephan SB, Moffett HF, McKnight LE, Ji W, Reiman D, et al. In situ programming of leukaemia-specific T cells using synthetic DNA nanocarriers. Nat Nanotech. 2017;12:813–20.

    Article  CAS  Google Scholar 

  67. Rurik JG, Tombácz I, Yadegari A, Méndez Fernández PO, Shewale SV, Li L, et al. CAR T cells produced in vivo to treat cardiac injury. Science. 2022;375:91–6.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Watanabe K, Nishikawa H. Engineering strategies for broad application of TCR-T- and CAR-T-cell therapies. Int Immunol. 2021;33:551–62.

    Article  PubMed  CAS  Google Scholar 

  69. Rath JA, Arber C. Engineering Strategies to Enhance TCR-Based Adoptive T Cell Therapy. Cells. 2020;9:1485.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Vazquez-Lombardi R, Jung JS, Schlatter FS, Mei A, Mantuano NR, Bieberich F, et al. High-throughput T cell receptor engineering by functional screening identifies candidates with enhanced potency and specificity. Immunity. 2022;55:1953–1966.e10.

    Article  PubMed  CAS  Google Scholar 

  71. Ng S, Tjhung KF, Paschal BM, Noren CJ, Derda R. Chemical Posttranslational Modification of Phage-Displayed Peptides. In: Derda R, editor. Peptide Libraries. Springer New York: New York, NY; 2015. p. 155–72. https://doi.org/10.1007/978-1-4939-2020-4_11.

  72. Moesslacher CS, Kohlmayr JM, Stelzl U. Exploring absent protein function in yeast: assaying post translational modification and human genetic variation. Microb Cell. 2021;8:164–83.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Esvelt KM, Carlson JC, Liu DR. A system for the continuous directed evolution of biomolecules. Nature. 2011;472:499–503.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, et al. Rapid generation of potent antibodies by autonomous hypermutation in yeast. Nat Chem Biol. 2021;17:1057–64.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Acknowledgements

Figures 1, 2, and 3 were created with BioRender.com and are used with permission of the copyright holder, Biorender.

Funding

The authors acknowledge funding from National Institutes of Health (R01EY031097) and an Allegheny Health Network-Johns Hopkins Cancer Research Fund award. M.K. and K.P. are recipients of National Science Foundation Graduate Research Fellowship Program awards.

Author information

Authors and Affiliations

Authors

Contributions

M.K., K.P., L.M.T., and J.B.S. wrote and revised the paper.

Corresponding author

Correspondence to Jamie B. Spangler.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kizerwetter, M., Pietz, K., Tomasovic, L.M. et al. Empowering gene delivery with protein engineering platforms. Gene Ther 30, 775–782 (2023). https://doi.org/10.1038/s41434-022-00379-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41434-022-00379-6

Search

Quick links