Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells

Abstract

Cell therapy approaches that employ engineered mammalian cells for on-demand production of therapeutic agents in the patient’s body are moving beyond proof-of-concept in translational medicine. The therapeutic cells can be customized to sense user-defined signals, process them, and respond in a programmable and predictable way. In this paper, we introduce the available tools and strategies employed to design therapeutic cells. Then, various approaches to control cell behaviors, including open-loop and closed-loop systems, are discussed. We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental disease models. Finally, we consider emerging technologies such as digital devices and their potential for incorporation into future cell-based therapies.

Keywords

synthetic biology / cell-based therapy / cell engineering / therapeutic gene expression / controllable genetic circuits

References

[1] Albinger N , Hartmann J , Ullrich E (2021) Current status and perspective of CAR-T and CAR-NK cell therapy trials in Germany. Gene Ther 65: 84- 94

[2] Ausländer D , Ausländer S , Charpin-El Hamri G , Sedlmayer F , Müller M , Frey O , Hierlemann A , Stelling J , Fussenegger M (2014) A synthetic multifunctional mammalian pH sensor and CO₂ transgene-control device. Mol Cell 55: 397- 408

[3] Bai P , Ye H , Xie M , Saxena P , Zulewski H , Charpin-El Hamri G , Djonov V , Fussenegger M (2016) A synthetic biology-based device prevents liver injury in mice. J Hepatol.

[4] Bai P , Liu Y , Xue S , Hamri GCE , Saxena P , Ye H , Xie M , Fussenegger M (2019) A fully human transgene switch to regulate therapeutic protein production by cooling sensation. Nat Med.

[5] Beyer HM , Naumann S , Weber W , Radziwill G (2015) Optogenetic control of signaling in mammalian cells. Biotechnol J.

[6] Bojar D , Scheller L , Hamri GCE , Xie M , Fussenegger M (2018) Caffeine-inducible gene switches controlling experimental diabetes. Nat Commun 9: 1- 10

[7] Bose S , Volpatti LR , Thiono D , Yesilyurt V , McGladrigan C , Tang Y , Facklam A , Wang A , Jhunjhunwala S , Veiseh O et al (2020) A retrievable implant for the long-term encapsulation and survival of therapeutic xenogeneic cells. Nat Biomed Eng 4: 814- 826

[8] Brown SA , Kovatchev BP , Raghinaru D , Lum JW , Buckingham BA , Kudva YC , Laffel LM , Levy CJ , Pinsker JE , Wadwa RP et al (2019) Six-month randomized, multicenter trial of closed-loop control in type 1 diabetes. N Engl J Med 381: 1707- 1717

[9] Caliendo F , Dukhinova M , Siciliano V (2019) Engineered cell-based therapeutics: synthetic biology meets immunology. Front Bioeng Biotechnol 7: 43

[10] Carpenter A , Paulsen I , Williams T (2018) Blueprints for biosensors:design, limitations, and applications. Genes (basel) 9: 375

[11] Chen Z , Wang J , Sun W , Archibong E , Kahkoska AR , Zhang X , Lu Y , Ligler FS , Buse JB , Gu Z (2018) Synthetic beta cells for fusionmediated dynamic insulin secretion. Nat Chem Biol 14: 86- 93

[12] Chmielewski M , Abken H (2015) TRUCKs: the fourth generation of CARs. Expert Opin Biol Ther.

[13] Cho JH , Collins JJ , Wong WW (2018) Universal chimeric antigen receptors for multiplexed and logical control of T cell responses. Cell 173: 1426- 1438.e11

[14] Choi BD , Yu X , Castano AP , Bouffard AA , Schmidts A , Larson RC , Bailey SR , Boroughs AC , Frigault MJ , Leick MB et al (2019) CART cells secreting BiTEs circumvent antigen escape without detectable toxicity. Nat Biotechnol 37: 1049- 1058

[15] Christiansen MG , Hornslien W , Schuerle PS , Schuerle S (2020) A possible inductive mechanism for magnetogenetics. bioRxiv.

[16] Desai T , Shea LD (2017) Advances in islet encapsulation technologies. Nat Rev Drug Discov.

[17] Dixon TA , Williams TC , Pretorius IS (2021) Sensing the future of bioinformational engineering. Nat Commun.

[18] Dufort CC , Paszek MJ , Weaver VM (2011) Balancing forces:architectural control of mechanotransduction. Nat Rev Mol Cell Biol.

[19] Eglen R , Reisine T (2011) Primary cells and stem cells in drug discovery: emerging tools for high-throughput screening. Assay Drug Dev Technol 9: 108- 124

[20] Fedorov VD , Themeli M , Sadelain M (2013) PD-1- and CTLA-4-based inhibitory chimeric antigen receptors (iCARs) divert off-target immunotherapy responses. Sci Transl Med.

[21] Gaj T , Sirk SJ , Shui S-L , Liu J (2016) Genome-editing technologies:principles and applications. Cold Spring Harb Perspect Biol 8: a023754

[22] He L , Zhang Y , Ma G , Tan P , Li Z , Zang S , Wu X , Jing J , Fang S , Zhou L et al (2015) Near-infrared photoactivatable control of Ca²⁺ signaling and optogenetic immunomodulation. Elife 4: e10024

[23] Israni DV , Li H-S , Gagnon KA , Sander JD , Roybal KT , Joung JK , Wong WW , Khalil AS (2021) Clinically-driven design of synthetic gene regulatory programs in human cells. bioRxiv.

[24] June CH , Sadelain M (2018) Chimeric antigen receptor therapy. N Engl J Med 379: 64- 73

[25] Kemmer C , Gitzinger M , Daoud-El Baba M , Djonov V , Stelling J , Fussenegger M (2010) Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol 28: 355- 360

[26] Khalil AS , Collins JJ (2010) Synthetic biology: applications come of age. Nat Rev Genet 11: 367- 379

[27] Kiel C , Yus E , Serrano L (2010) Engineering signal transduction pathways. Cell.

[28] Kim J , Campbell AS , de Ávila BEF , Wang J (2019) Wearable biosensors for healthcare monitoring. Nat Biotechnol.

[29] Kitada T , DiAndreth B , Teague B , Weiss R (2018) Programming gene and engineered-cell therapies with synthetic biology. Science 359: 1067

[30] Klichinsky M , Ruella M , Shestova O , Lu XM , Best A , Zeeman M , Schmierer M , Gabrusiewicz K , Anderson NR , Petty NE et al (2020) Human chimeric antigen receptor macrophages for cancer immunotherapy. Nat Biotechnol 38: 947- 953

[31] Kloss CC , Condomines M , Cartellieri M , Bachmann M , Sadelain M (2013) Combinatorial antigen recognition with balanced signaling promotes selective tumor eradication by engineered T cells. Nat Biotechnol 31: 71- 75

[32] Kojima R , Aubel D , Fussenegger M (2016) Toward a world of theranostic medication: programming biological sentinel systems for therapeutic intervention. Adv Drug Deliv Rev.

[33] Kojima R , Scheller L , Fussenegger M (2018) Nonimmune cells equipped with T-cell-receptor-like signaling for cancer cell ablation. Nat Chem Biol 14: 42- 49

[34] Kojima R , Aubel D , Fussenegger M (2020) Building sophisticated sensors of extracellular cues that enable mammalian cells to work as “doctors” in the body. Cell Mol Life Sci.

[35] Kolar K , Weber W (2017) Synthetic biological approaches to optogenetically control cell signaling. Curr Opin Biotechnol.

[36] Krawczyk K , Xue S , Buchmann P , Charpin-El-Hamri G , Saxena P , Hussherr MD , Shao J , Ye H , Xie M , Fussenegger M (2020) Electrogenetic cellular insulin release for real-time glycemic control in type 1 diabetic mice. Science 368: 993- 1001

[37] Li J , Liang JY , Laken SJ , Langer R , Traverso G (2020) Clinical opportunities for continuous biosensing and closed-loop therapies. Trends Chem.

[38] Lim WA , June CH (2017) Review the principles of engineering immune cells to treat cancer. Cell 168: 724- 740

[39] Liu Y , Bai P , Woischnig AK , Charpin-El Hamri G , Ye H , Folcher M , Xie M , Khanna N , Fussenegger M (2018) Immunomimetic designer cells protect mice from MRSA infection. Cell 174: 259- 270

[40] Lohmueller J , Butchy A , Tivon Y , Kvorjak M , Miskov-Zivanov N , Deiters A , Finn O (2020) Post-translational covalent assembly of CAR and synNotch receptors for programmable antigen targeting. bioRxiv.

[41] Maggio I , Gonçalves MAFV (2015) Genome editing at the crossroads of delivery, specificity, and fidelity. Trends Biotechnol 33: 280- 291

[42] Mansouri M , Berger P (2018) Multigene delivery in mammalian cells:recent advances and applications. Biotechnol Adv.

[43] Mansouri M , Bellon-Echeverria I , Rizk A , Ehsaei Z , Cianciolo Cosentino C , Silva CS , Xie Y , Boyce FM , Davis MW et al (2016) Highly efficient baculovirus-mediated multigene delivery in primary cells. Nat Commun 7: 11529

[44] Mansouri M , Strittmatter T , Fussenegger M (2019) Light-controlled mammalian cells and their therapeutic applications in synthetic biology. Adv Sci (weinh).

[45] Mansouri M , Hussherr M-D , Strittmatter T , Buchmann P , Xue S , Camenisch G , Fussenegger M (2021a) Smart-watch-programmed green-light-operated percutaneous control of therapeutic transgenes. Nat Commun 12: 3388

[46] Mansouri M , Xue S , Hussherr M-D , Strittmatter T , Camenisch G , Fussenegger M (2021b) Smartphone-flashlight-mediated remote control of rapid insulin secretion restores glucose homeostasis in experimental type-1 diabetes. Small.

[47] Marx V (2015) Cell biology: delivering tough cargo into cells. Nat Methods 13: 37- 40

[48] Matsunaga S , Jeremiah SS , Miyakawa K , Kurotaki D , Shizukuishi S , Watashi K , Nishitsuji H , Kimura H , Tamura T , Yamamoto N et al (2020) Engineering cellular biosensors with customizable antiviral responses targeting hepatitis B virus. Science 23: 100867

[49] Maurisse R , De Semir D , Emamekhoo H , Bedayat B , Abdolmohammadi A , Parsi H , Gruenert DC (2010) Comparative transfection of DNA into primary and transformed mammalian cells from different lineages. BMC Biotechnol 10: 9

[50] McClune CJ , Alvarez-Buylla A , Voigt CA , Laub MT (2019) Engineering orthogonal signalling pathways reveals the sparse occupancy of sequence space. Nature 574: 702- 706

[51] Miller IC , Gamboa Castro M , Maenza J , Weis JP , Kwong GA (2018) Remote control of mammalian cells with heat-triggered gene switches and photothermal pulse trains. ACS Synth Biol 7: 1167- 1173

[52] Morsut L , Roybal KTKT , Xiong X , Gordley RM , Coyle SM , Thomson M , Lim WAWA (2016) Engineering customized cell sensing and response behaviors using synthetic notch receptors. Cell 164: 780- 791

[53] Mukherjee A , Repina NA , Schaffer DV , Kane RS (2017) Optogenetic tools for cell biological applications. J Thorac Dis.

[54] Müller K , Naumann S , Weber W , Zurbriggen MD (2015) Optogenetics for gene expression in mammalian cells. Biol Chem.

[55] Mure LSS , Hatori M , Zhu Q , Demas J , Kim IMM , Nayak SKK , Panda S (2016) Melanopsin-encoded response properties of intrinsically photosensitive retinal ganglion cells. Neuron 90: 1016- 1027

[56] Neelapu SS , Tummala S , Kebriaei P , Wierda W , Gutierrez C , Locke FL , Komanduri KV , Lin Y , Jain N , Daver N et al (2018) Chimeric antigen receptor T-cell therapy-assessment and management of toxicities. Nat Rev Clin Oncol.

[57] Pan Y , Yoon S , Sun J , Huang Z , Lee C , Allen M , Wu Y , Chang YJ , Sadelain M , Kirk Shung K et al (2018) Mechanogenetics for the remote and noninvasive control of cancer immunotherapy. Proc Natl Acad Sci USA 115: 992- 997

[58] Papapetrou EP , Schambach A (2016) Gene insertion into genomic safe harbors for human gene therapy. Mol Ther.

[59] Park JS , Rhau B , Hermann A , McNally KA , Zhou C , Gong D , Weiner OD , Conklin BR , Onuffer J , Lim WA (2014) Synthetic control of mammalian-cellmotility by engineering chemotaxis to anorthogonal bioinert chemical signal. Proc Natl Acad Sci USA 111: 5896- 5901

[60] Polonsky KS , Given BD , Van Cauter E (1988) Twenty-four-hour profiles and pulsatile patterns of insulin secretion in normal and obese subjects. J Clin Invest 81: 442- 448

[61] Rafiq S , Hackett CS , Brentjens RJ (2020) Engineering strategies to overcome the current roadblocks in CAR T cell therapy. Nat Rev Clin Oncol 1: 1

[62] Rivera VM , Wang X , Wardwell S , Courage NL , Volchuk A , Keenan T , Holt DA , Gilman M , Orci L , Cerasoli F et al (2000) Regulation of protein secretion through controlled aggregation in the endoplasmic reticulum. Science 287: 826- 830

[63] Rössger K , Charpin-El-Hamri G , Fussenegger M (2013a) A closedloop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun 4: 1- 9

[64] Rössger K , Charpin-El Hamri G , Fussenegger M (2013b) Reward-based hypertension control by a synthetic brain-dopamine interface. Proc Natl Acad Sci USA 110: 18150- 18155

[65] Roybal KT , Lim WA (2017) Synthetic immunology: hacking immune cells to expand their therapeutic capabilities. Annu Rev Immunol.

[66] Roybal KT , Rupp LJ , Morsut L , Walker WJ , McNally KA , Park JS , Lim WA , Box C , Eccles SA , Maher J et al (2016a) Precision tumor recognition by T cells with combinatorial antigen-sensing circuits. Cell 164: 770- 779

[67] Roybal KT , Williams JZ , Morsut L , Rupp LJ , Kolinko I , Choe JH , Walker WJ , McNally KA , Lim WA , Rupp LJ et al (2016b) Engineering T cells with customized therapeutic response programs using synthetic notch receptors. Cell.

[68] Saxena P , Hamri GCE , Folcher M , Zulewski H , Fussenegger M (2016a) Synthetic gene network restoring endogenous pituitary-thyroid feedback control in experimental Graves’ disease. Proc Natl Acad Sci USA 113: 1244- 1249

[69] Saxena P , Heng BC , Bai P , Folcher M , Zulewski H , Fussenegger M (2016b) A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting beta-like cells. Nat Commun 7: 1- 14

[70] Saxena P , Bojar D , Zulewski H , Fussenegger M (2017) Generation of glucose-sensitive insulin-secreting beta-like cells from human embryonic stem cells by incorporating a synthetic lineage-control network. J Biotechnol 259: 39- 45

[71] Scheller L , Fussenegger M (2019) From synthetic biology to human therapy: engineered mammalian cells. Curr Opin Biotechnol 58: 108- 119

[72] Scheller L , Strittmatter T , Fuchs D , Bojar D , Fussenegger M (2018) Generalized extracellular molecule sensor platform for programming cellular behavior. Nat Chem Biol 14: 723- 729

[73] Schmidt P , Raftery MJ , Pecher G (2021) Engineering NK cells for CAR therapy-recent advances in gene transfer methodology. Front Immunol.

[74] Schukur L , Fussenegger M (2016) Engineering of synthetic gene circuits for (re-)balancing physiological processes in chronic diseases. Wiley Interdiscip Rev Syst Biol Med 8: 402- 422

[75] Schukur L , Geering B , Charpin-El Hamri G , Fussenegger M (2015) Implantable synthetic cytokine converter cells with AND-gate logic treat experimental psoriasis. Sci Transl Med 7: 318318ra201

[76] Sedlmayer F , Hell D , Müller M , Ausländer D , Fussenegger M (2018) Designer cells programming quorum-sensing interference with microbes. Nat Commun 9: 1- 13

[77] Shao J , Xue S , Yu G , Yu Y , Yang X , Bai Y , Zhu S , Yang L , Yin J , Wang Y et al (2017) Smartphone-controlled optogenetically engineered cells enable semiautomatic glucose homeostasis in diabetic mice. Sci Transl Med 9: eaal2298

[78] Sim I (2019) Mobile devices and health. N Engl J Med.

[79] Slattery D , Choudhary P (2017) Clinical use of continuous glucose monitoring in adults with type 1 diabetes. Diabetes Technol Ther.

[80] Stanley SA , Gagner JE , Damanpour S , Yoshida M , Dordick JS , Friedman JM (2012) Radio-wave heating of iron oxide nanopar-ticles can regulate plasma glucose in mice. Science 336: 604- 608

[81] Steinhubl SR , Muse ED , Topol EJ (2015) The emerging field of mobile health. Sci. Transl. Med.

[82] Su Y , Huang X , Huang Z , Huang T , Li T , Fan H , Zhang K , Yi C (2020) Early but not delayed optogenetic RAF activation promotes astrocytogenesis in mouse neural progenitors. J Mol Biol 432: 4358- 4368

[83] Sun J , Lei L , Tsai CM , Wang Yi , Shi Y , Ouyang M , Lu S , Seong J , Kim TJ , Wang P et al (2017) Engineered proteins with sensing and activating modules for automated reprogramming of cellular functions. Nat Commun 8: 1- 10

[84] Tastanova A , Folcher M , Müller M , Camenisch G , Ponti A , Horn T , Tikhomirova MS , Fussenegger M (2018) Synthetic biology-based cellular biomedical tattoo for detection of hypercalcemia associated with cancer. Sci Transl Med 10: 8562

[85] Toda S , Blauch LR , Tang SKY , Morsut L , Lim WA (2018) Programming self-organizing multicellular structures with synthetic cellcell signaling. Science 361: 156- 162

[86] Wang X , Chen X , Yang Y (2012) Spatiotemporal control of gene expression by a light-switchable transgene system. Nat Methods 9: 266- 269

[87] Wang H , Xie M , Charpin-El Hamri G , Ye H , Fussenegger M (2018a) Treatment of chronic pain by designer cells controlled by spearmint aromatherapy. Nat Biomed Eng 2: 114- 123

[88] Wang Y , Wang M , Dong K , Ye H (2018b) Engineering mammalian designer cells for the treatment of metabolic diseases. Biotechnol J 13: 1700160

[89] Weber W , Fussenegger M (2004) Inducible gene expression in mammalian cells and mice. Methods Mol Biol 267: 451- 466

[90] Xie M , Fussenegger M (2015) Mammalian designer cells: engineering principles and biomedical applications. Biotechnol J.

[91] Xie M , Fussenegger M (2018) Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat Rev Mol Cell Biol.

[92] Xie M , Haellman V , Fussenegger M (2016a) Synthetic biology -application-oriented cell engineering. Curr Opin Biotechnol.

[93] Xie M , Ye H , Wang H , Charpin-El Hamri G , Lormeau C , Saxena P , Stelling J , Fussenegger M (2016b) β-cell-mimetic designer cells provide closed-loop glycemic control. Science 354: 1296- 1301

[94] Xue S , Yin J , Shao J , Yu Y , Yang L , Wang Y , Xie M , Fussenegger M , Ye H (2017) A synthetic-biology-inspired therapeutic strategy for targeting and treating hepatogenous diabetes. Mol Ther 25: 443- 455

[95] Yamada M , Nagasaki SC , Ozawa T , Imayoshi I (2020) Lightmediated control of gene expression in mammalian cells. Neurosci Res.

[96] Ye H , Baba MDE , Peng RW , Fussenegger M (2011) A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332: 1565- 1568

[97] Yip A , Webster RM (2018) The market for chimeric antigen receptor T cell therapies. Nat Rev Drug Discov 17: 161- 162

[98] Zhang F , Tzanakakis ES (2019) Amelioration of diabetes in a murine model upon transplantation of pancreatic β-cells with optogenetic control of cyclic adenosine monophosphate. ACS Synth Biol 8: 2248- 2255

[99] Zhu L , Wu Y , Yoon CW , Wang Y (2020) Mechanogenetics for cellular engineering and cancer immunotherapy. Curr Opin Biotechnol.

RIGHTS & PERMISSIONS

2022 The Author(s)