Nielsen, J. & Keasling, J. D. Engineering cellular metabolism. Cell 164, 1185–1197 (2016).
Ajikumar, P. K. et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330, 70–74 (2010).
Galanie, S., Thodey, K., Trenchard, I. J., Filsinger Interrante, M. & Smolke, C. D. Complete biosynthesis of opioids in yeast. Science 349, 1095–1100 (2015).
Paddon, C. J. et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496, 528–532 (2013).
Wurm, F. M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 22, 1393–1398 (2004).
Eichenberger, M. et al. Metabolic engineering of Saccharomyces cerevisiae for de novo production of dihydrochalcones with known antioxidant, antidiabetic, and sweet tasting properties. Metab. Eng. 39, 80–89 (2017).
Atsumi, S., Hanai, T. & Liao, J. C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86–89 (2008).
Yang, X., Xu, M. & Yang, S. T. Metabolic and process engineering of Clostridium cellulovorans for biofuel production from cellulose. Metab. Eng. 32, 39–48 (2015).
Widmaier, D. M. et al. Engineering the Salmonella type III secretion system to export spider silk monomers. Mol. Syst. Biol. 5, 309 (2009).
Auslander, S., Auslander, D. & Fussenegger, M. Synthetic biology — the synthesis of biology. Angew. Chem. Int. Ed Engl. 56, 6396–6419 (2017).
Maude, S. L. et al. Chimeric antigen receptor T cells for sustained remissions in leukemia. N. Engl. J. Med. 371, 1507–1517 (2014).
Porter, D. L., Levine, B. L., Kalos, M., Bagg, A. & June, C. H. Chimeric antigen receptor-modified T cells in chronic lymphoid leukemia. N. Engl. J. Med. 365, 725–733 (2011).
Fesnak, A. D., June, C. H. & Levine, B. L. Engineered T cells: the promise and challenges of cancer immunotherapy. Nat. Rev. Cancer 16, 566–581 (2016).
Chakravarti, D. & Wong, W. W. Synthetic biology in cell-based cancer immunotherapy. Trends Biotechnol. 33, 449–461 (2015).
Culler, S. J., Hoff, K. G. & Smolke, C. D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330, 1251–1255 (2010).
Paek, K. Y. et al. Translation initiation mediated by RNA looping. Proc. Natl Acad. Sci. USA 112, 1041–1046 (2015).
Van Etten, J. et al. Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J. Biol. Chem. 287, 36370–36383 (2012).
Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).
Ipsaro, J. J. & Joshua-Tor, L. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat. Struct. Mol. Biol. 22, 20–28 (2015).
Greber, D., El-Baba, M. D. & Fussenegger, M. Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch. Nucleic Acids Res. 36, e101 (2008).
Fux, C. et al. Streptogramin- and tetracycline-responsive dual regulated expression of p27(Kip1) sense and antisense enables positive and negative growth control of Chinese hamster ovary cells. Nucleic Acids Res. 29, E19 (2001).
Niopek, D. et al. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells. Nat. Commun. 5, 4404 (2014).
Beyer, H. M. et al. Red light-regulated reversible nuclear localization of proteins in mammalian cells and zebrafish. ACS Synth. Biol. 4, 951–958 (2015).
Niopek, D., Wehler, P., Roensch, J., Eils, R. & Di Ventura, B. Optogenetic control of nuclear protein export. Nat. Commun. 7, 10624 (2016).
Chen, D., Gibson, E. S. & Kennedy, M. J. A light-triggered protein secretion system. J. Cell Biol. 201, 631–640 (2013).
Spiltoir, J. I., Strickland, D., Glotzer, M. & Tucker, C. L. Optical control of peroxisomal trafficking. ACS Synth. Biol. 5, 554–560 (2016).
Finley, D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu. Rev. Biochem. 78, 477–513 (2009).
Janse, D. M., Crosas, B., Finley, D. & Church, G. M. Localization to the proteasome is sufficient for degradation. J. Biol. Chem. 279, 21415–21420 (2004).
Sandri, M. et al. Foxo transcription factors induce the atrophy-related ubiquitin ligase atrogin-1 and cause skeletal muscle atrophy. Cell 117, 399–412 (2004).
Macian, F. NFAT proteins: key regulators of T cell development and function. Nat. Rev. Immunol. 5, 472–484 (2005).
Keeley, M. B., Busch, J., Singh, R. & Abel, T. TetR hybrid transcription factors report cell signaling and are inhibited by doxycycline. Biotechniques 39, 529–536 (2005).
Mishra, D., Rivera, P. M., Lin, A., Del Vecchio, D. & Weiss, R. A load driver device for engineering modularity in biological networks. Nat. Biotechnol. 32, 1268–1275 (2014).
Garg, A., Lohmueller, J. J., Silver, P. A. & Armel, T. Z. Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res. 40, 7584–7595 (2012).
Thakore, P. I., Black, J. B., Hilton, I. B. & Gersbach, C. A. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods 13, 127–137 (2016).
Stanton, B. C. et al. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth. Biol. 3, 880–891 (2014).
Esvelt, K. M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 1116–1121 (2013).
Chen, B. et al. Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res. 44, e75 (2016).
Briner, A. E. et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell 56, 333–339 (2014). This paper analyses different structural motifs of gRNAs in great detail and provides an excellent resource for the design of novel CRISPR–Cas-dependent functions, such as the engineering of scRNA for multiplexed transcriptional regulation (see also reference 39) or the construction of signal conductors (see also reference 40).
Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339–350 (2015).
Liu, Y. et al. Directing cellular information flow via CRISPR signal conductors. Nat. Methods 13, 938–944 (2016).
Kashida, S., Inoue, T. & Saito, H. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation. Nucleic Acids Res. 40, 9369–9378 (2012).
Perli, S. D., Cui, C. H. & Lu, T. K. Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353, aag0511 (2016).
Muller, K., Zurbriggen, M. D. & Weber, W. An optogenetic upgrade for the Tet-OFF system. Biotechnol. Bioeng. 112, 1483–1487 (2015).
Nihongaki, Y., Kawano, F., Nakajima, T. & Sato, M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol. 33, 755–760 (2015).
Neddermann, P. et al. A novel, inducible, eukaryotic gene expression system based on the quorum-sensing transcription factor TraR. EMBO Rep. 4, 159–165 (2003).
Auslander, S. & Fussenegger, M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol. 31, 155–168 (2013).
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. 17, 5–15 (2016).
Khalil, A. S. et al. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150, 647–658 (2012).
Schukur, L. & Fussenegger, M. Engineering of synthetic gene circuits for (re-)balancing physiological processes in chronic diseases. Wiley Interdiscip. Rev. Syst. Biol. Med. 8, 402–422 (2016).
Heng, B. C., Aubel, D. & Fussenegger, M. G protein-coupled receptors revisited: therapeutic applications inspired by synthetic biology. Annu. Rev. Pharmacol. Toxicol. 54, 227–249 (2014).
Auslander, S. & Fussenegger, M. Synthetic RNA-based switches for mammalian gene expression control. Curr. Opin. Biotechnol. 48, 54–60 (2017).
Chappell, J., Watters, K. E., Takahashi, M. K. & Lucks, J. B. A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Curr. Opin. Chem. Biol. 28, 47–56 (2015).
Deans, T. L., Cantor, C. R. & Collins, J. J. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130, 363–372 (2007).
Karlsson, M. et al. Pharmacologically controlled protein switch for ON-OFF regulation of growth factor activity. Sci. Rep. 3, 2716 (2013).
Park, J. S. et al. Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal. Proc. Natl Acad. Sci. USA 111, 5896–5901 (2014).
Nissim, L. et al. Synthetic RNA-based immunomodulatory gene circuits for cancer immunotherapy. Cell 171, 1138–1150.e15 (2017). This work uses lentiviral delivery of synthetic gene circuits in mice to illustrate a therapeutic strategy building on the concept of cancer biocomputers (see also references 191 and 192) and represents an important step towards clinical application.
Morsut, L. et al. Engineering customized cell sensing and response behaviors using synthetic Notch receptors. Cell 164, 780–791 (2016). By incorporating an antibody domain and a synthetic transcription factor into the modular framework of the Notch receptor, the authors of this study introduce a novel gene switch design for sensing direct cell contacts with programmable transgene readouts in neurons and T lymphocytes.
Baeumler, T. A., Ahmed, A. A. & Fulga, T. A. Engineering synthetic signaling pathways with programmable dCas9-based chimeric receptors. Cell Rep. 20, 2639–2653 (2017).
Barnea, G. et al. The genetic design of signaling cascades to record receptor activation. Proc. Natl Acad. Sci. USA 105, 64–69 (2008).
Schwarz, K. A., Daringer, N. M., Dolberg, T. B. & Leonard, J. N. Rewiring human cellular input-output using modular extracellular sensors. Nat. Chem. Biol. 13, 202–209 (2017).
Green, A. A., Silver, P. A., Collins, J. J. & Yin, P. Toehold switches: de-novo-designed regulators of gene expression. Cell 159, 925–939 (2014).
Beisel, C. L., Chen, Y. Y., Culler, S. J., Hoff, K. G. & Smolke, C. D. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res. 39, 2981–2994 (2011).
Auslander, S. et al. A general design strategy for protein-responsive riboswitches in mammalian cells. Nat. Methods 11, 1154–1160 (2014).
Bonger, K. M., Rakhit, R., Payumo, A. Y., Chen, J. K. & Wandless, T. J. General method for regulating protein stability with light. ACS Chem. Biol. 9, 111–115 (2014).
Strickland, D. et al. Rationally improving LOV domain-based photoswitches. Nat. Methods 7, 623–626 (2010).
Levskaya, A., Weiner, O. D., Lim, W. A. & Voigt, C. A. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997–1001 (2009).
Hughes, R. M. et al. Optogenetic apoptosis: light-triggered cell death. Angew. Chem. Int. Ed. 54, 12064–12068 (2015).
Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6, 917–922 (2009).
Kawano, F., Suzuki, H., Furuya, A. & Sato, M. Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins. Nat. Commun. 6, 6256 (2015).
Wu, Y. I. et al. A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461, 104–108 (2009).
Spiltoir, J. I., Strickland, D., Glotzer, M. & Tucker, C. L. Optical control of peroxisomal trafficking. ACS Synth. Biol. 5, 554–560 (2016).
Renicke, C., Schuster, D., Usherenko, S., Essen, L. O. & Taxis, C. A. LOV2 domain-based optogenetic tool to control protein degradation and cellular function. Chem. Biol. 20, 619–626 (2013).
Fukuda, N., Matsuda, T. & Nagai, T. Optical control of the Ca2+ concentration in a live specimen with a genetically encoded Ca2+-releasing molecular tool. ACS Chem. Biol. 9, 1197–1203 (2014).
Wang, Y. H., Wei, K. Y. & Smolke, C. D. Synthetic biology: advancing the design of diverse genetic systems. Annu. Rev. Chem. Biomol. Eng. 4, 69–102 (2013).
Kahn, M. Can we safely target the WNT pathway? Nat. Rev. Drug Discov. 13, 513–532 (2014).
Metcalfe, C., Mendoza-Topaz, C., Mieszczanek, J. & Bienz, M. Stability elements in the LRP6 cytoplasmic tail confer efficient signalling upon DIX-dependent polymerization. J. Cell Sci. 123, 1588–1599 (2010).
Bugaj, L. J., Choksi, A. T., Mesuda, C. K., Kane, R. S. & Schaffer, D. V. Optogenetic protein clustering and signaling activation in mammalian cells. Nat. Methods 10, 249–252 (2013).
Wehr, M. C. et al. Monitoring regulated protein-protein interactions using split TEV. Nat. Methods 3, 985–993 (2006).
Copeland, M. F., Politz, M. C., Johnson, C. B., Markley, A. L. & Pfleger, B. F. A transcription activator-like effector (TALE) induction system mediated by proteolysis. Nat. Chem. Biol. 12, 254–260 (2016).
Lapique, N. & Benenson, Y. Digital switching in a biosensor circuit via programmable timing of gene availability. Nat. Chem. Biol. 10, 1020–1027 (2014).
Prochazka, L., Angelici, B., Haefliger, B. & Benenson, Y. Highly modular bow-tie gene circuits with programmable dynamic behaviour. Nat. Commun. 5, 4729 (2014).
Muller, M. et al. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat. Chem. Biol. 13, 309–316 (2017).
Weinberg, B. H. et al. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat. Biotechnol. 35, 453–462 (2017). Capitalizing on a selection of ten orthogonal site-specific recombinases, the authors programme single promoter-driven transcription units into complex Boolean calculators that process different recombinase-specific input signals according to half-adder or half-subtractor (two inputs) and full-adder or full-subtractor (three inputs) logics.
Green, A. A. et al. Complex cellular logic computation using ribocomputing devices. Nature 548, 117–121 (2017). By re-engineering the toehold switch (see reference 61) to become conditionally activated by multiple trigger RNAs, the authors demonstrate that any complex (bio)computational task can be programmed on the basis of two-input AND, OR and NOT logic gates.
Burrill, D. R. & Silver, P. A. Making cellular memories. Cell 140, 13–18 (2010).
Covert, M. W., Leung, T. H., Gaston, J. E. & Baltimore, D. Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science 309, 1854–1857 (2005).
Myhrvold, C., Kotula, J. W., Hicks, W. M., Conway, N. J. & Silver, P. A. A distributed cell division counter reveals growth dynamics in the gut microbiota. Nat. Commun. 6, 10039 (2015).
Weber, W. et al. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl Acad. Sci. USA 104, 2643–2648 (2007).
Kramer, B. P. & Fussenegger, M. Hysteresis in a synthetic mammalian gene network. Proc. Natl Acad. Sci. USA 102, 9517–9522 (2005).
Hussain, F. et al. Engineered temperature compensation in a synthetic genetic clock. Proc. Natl Acad. Sci. USA 111, 972–977 (2014).
Folcher, M., Xie, M., Spinnler, A. & Fussenegger, M. Synthetic mammalian trigger-controlled bipartite transcription factors. Nucleic Acids Res. 41, e134 (2013). Using different hybrid transcription factors composed of multiple TetR family repressors, this work provides an in-depth characterization of the most widely used trans-regulators in synthetic biology (for example, TetR, VanR, ScbR or TtgR) and discusses important design principles for programming complex transgene functions.
Burrill, D. R., Inniss, M. C., Boyle, P. M. & Silver, P. A. Synthetic memory circuits for tracking human cell fate. Genes Dev. 26, 1486–1497 (2012).
Yao, G., Tan, C., West, M., Nevins, J. R. & You, L. Origin of bistability underlying mammalian cell cycle entry. Mol. Syst. Biol. 7, 485 (2011).
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000). This paper describes a design of a genetic toggle switch, which inaugurated the modern era of synthetic biology featuring the development of a standardized and reusable ‘engineering language’ to programme complex cell functions.
Kobayashi, H. et al. Programmable cells: interfacing natural and engineered gene networks. Proc. Natl Acad. Sci. USA 101, 8414–8419 (2004).
Kramer, B. P. et al. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 22, 867–870 (2004).
Graf, T. & Enver, T. Forcing cells to change lineages. Nature 462, 587–594 (2009).
Bonnet, J., Subsoontorn, P. & Endy, D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl Acad. Sci. USA 109, 8884–8889 (2012). In contrast to most other permanent memory devices, where each data register can be written by a site-specific recombinase only once, this work shows that additional expression of an excisionase in bacteria to restore the recombinase-specific recognition sites can generate resettable memory registers.
Yang, L. et al. Permanent genetic memory with >1-byte capacity. Nat. Methods 11, 1261–1266 (2014).
Kalhor, R., Mali, P. & Church, G. M. Rapidly evolving homing CRISPR barcodes. Nat. Methods 14, 195–200 (2017).
Frieda, K. L. et al. Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107–111 (2017).
Farzadfard, F. & Lu, T. K. Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 1256272 (2014).
Tamsir, A., Tabor, J. J. & Voigt, C. A. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469, 212–215 (2011).
Wong, A., Wang, H., Poh, C. L. & Kitney, R. I. Layering genetic circuits to build a single cell, bacterial half adder. BMC Biol. 13, 40 (2015).
Auslander, S., Auslander, D., Muller, M., Wieland, M. & Fussenegger, M. Programmable single-cell mammalian biocomputers. Nature 487, 123–127 (2012).
Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599–603 (2013).
Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).
Imanishi, M. et al. Construction of a rhythm transfer system that mimics the cellular clock. ACS Chem. Biol. 7, 1817–1821 (2012).
Chilov, D. & Fussenegger, M. Toward construction of a self-sustained clock-like expression system based on the mammalian circadian clock. Biotechnol. Bioeng. 87, 234–242 (2004).
Fung, E. et al. A synthetic gene-metabolic oscillator. Nature 435, 118–122 (2005).
Toettcher, J. E., Mock, C., Batchelor, E., Loewer, A. & Lahav, G. A synthetic-natural hybrid oscillator in human cells. Proc. Natl Acad. Sci. USA 107, 17047–17052 (2010).
Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).
Atkinson, M. R., Savageau, M. A., Myers, J. T. & Ninfa, A. J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113, 597–607 (2003).
Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008). This work reports the key principles for the design of an essentially ideal synthetic oscillator; robust, persistent and tunable gene oscillations are enabled by a positive feedback module that activates all modules in a gene circuit and a slower-acting negative feedback module that represses the very same targets.
Mondragon-Palomino, O., Danino, T., Selimkhanov, J., Tsimring, L. & Hasty, J. Entrainment of a population of synthetic genetic oscillators. Science 333, 1315–1319 (2011).
Weber, W. et al. Streptomyces-derived quorum-sensing systems engineered for adjustable transgene expression in mammalian cells and mice. Nucleic Acids Res. 31, e71 (2003).
You, L., Cox, R. S. 3rd, Weiss, R. & Arnold, F. H. Programmed population control by cell–cell communication and regulated killing. Nature 428, 868–871 (2004).
Din, M. O. et al. Synchronized cycles of bacterial lysis for in vivo delivery. Nature 536, 81–85 (2016). In this study, the pulse-like gene expression dynamics of the synthetic quorum-based oscillator are repurposed to programme S. Typhimurium for self-autonomous cancer targeting, lysis and drug release, resulting in a 50% increase in survival in a mouse model of colorectal cancer when combined with common clinical chemotherapy.
Liu, C. et al. Sequential establishment of stripe patterns in an expanding cell population. Science 334, 238–241 (2011).
Danino, T., Mondragon-Palomino, O., Tsimring, L. & Hasty, J. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).
Ryback, B. M. et al. Design and analysis of a tunable synchronized oscillator. J. Biol. Eng. 7, 26 (2013).
Prindle, A. et al. A sensing array of radically coupled genetic ‘biopixels’. Nature 481, 39–44 (2011).
Tigges, M., Marquez-Lago, T. T., Stelling, J. & Fussenegger, M. A tunable synthetic mammalian oscillator. Nature 457, 309–312 (2009).
Tigges, M., Denervaud, N., Greber, D., Stelling, J. & Fussenegger, M. A synthetic low-frequency mammalian oscillator. Nucleic Acids Res. 38, 2702–2711 (2010).
Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
Greber, D. & Fussenegger, M. An engineered mammalian band-pass network. Nucleic Acids Res. 38, e174 (2010).
Saxena, P. et al. A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting beta-like cells. Nat. Commun. 7, 11247 (2016). In this study, a synthetic gene circuit, termed a lineage control network, based on a vanillic-acid-regulated band-pass filter controlling cell stage-specific NGN3 expression coupled to PDX1 repression and MAFA activation differentiates pancreatic progenitor cells into mature β-like cells with a higher efficiency than could be achieved with conventional methods such as ectopic overexpression of PDX1, NGN3 and MAFA (see references 142 and 143) or chemical cultivation methods (see references 144 and 145).
Kolar, K. et al. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. BMC Syst. Biol. 9, 97 (2015).
Bacchus, W. et al. Synthetic two-way communication between mammalian cells. Nat. Biotechnol. 30, 991–996 (2012).
Weber, W., Daoud-El Baba, M. & Fussenegger, M. Synthetic ecosystems based on airborne inter- and intrakingdom communication. Proc. Natl Acad. Sci. USA 104, 10435–10440 (2007).
Kojima, R., Scheller, L. & Fussenegger, M. Nonimmune cells equipped with T cell-receptor-like signaling for cancer cell ablation. Nat. Chem. Biol. 14, 42–49 (2018).
Skjoedt, M. L. et al. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast. Nat. Chem. Biol. 12, 951–958 (2016).
Slomovic, S. & Collins, J. J. DNA sense-and-respond protein modules for mammalian cells. Nat. Methods 12, 1085–1090 (2015).
Schena, A., Griss, R. & Johnsson, K. Modulating protein activity using tethered ligands with mutually exclusive binding sites. Nat. Commun. 6, 7830 (2015).
Pardee, K. et al. Paper-based synthetic gene networks. Cell 159, 940–954 (2014). This work shows that synthetic gene circuits not only operate in living cells but also retain most of their functionality when the relevant coding genes and cell lysates are incorporated into abiotic material, such as paper.
Gootenberg, J. S. et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438–442 (2017).
Griss, R. et al. Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring. Nat. Chem. Biol. 10, 598–603 (2014).
Auslander, D. et al. A designer cell-based histamine-specific human allergy profiler. Nat. Commun. 5, 4408 (2014).
Schukur, L., Geering, B. & Fussenegger, M. Human whole-blood culture system for ex vivo characterization of designer-cell function. Biotechnol. Bioeng. 113, 588–597 (2016).
Courbet, A., Endy, D., Renard, E., Molina, F. & Bonnet, J. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Sci. Transl Med. 7, 289ra83 (2015).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006). This milestone paper, showing that ectopic overexpression of the master transcription factors OCT4, SOX2, KLF4 and MYC is sufficient to confer a stem cell-like identity upon any somatic cell type, features the Nobel Prize-winning discovery of induced pluripotent stem cells.
Ariyachet, C. et al. Reprogrammed stomach tissue as a renewable source of functional beta cells for blood glucose regulation. Cell Stem Cell 18, 410–421 (2016).
Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J. & Melton, D. A. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature 455, 627–632 (2008).
Zhu, S. et al. Human pancreatic beta-like cells converted from fibroblasts. Nat. Commun. 7, 10080 (2016).
Pagliuca, F. W. et al. Generation of functional human pancreatic beta cells in vitro. Cell 159, 428–439 (2014).
Teague, B. P., Guye, P. & Weiss, R. Synthetic morphogenesis. Cold Spring Harb. Perspect. Biol. 8, a023929 (2016).
Weber, W. et al. A synthetic mammalian gene circuit reveals antituberculosis compounds. Proc. Natl Acad. Sci. USA 105, 9994–9998 (2008).
Menzel, A., Gubeli, R. J., Guder, F., Weber, W. & Zacharias, M. Detection of real-time dynamics of drug-target interactions by ultralong nanowalls. Lab Chip 13, 4173–4179 (2013).
Sedlmayer, F., Jaeger, T., Jenal, U. & Fussenegger, M. Quorum-quenching human designer cells for closed-loop control of Pseudomonas aeruginosa biofilms. Nano Lett. 17, 5043–5050 (2017).
Saeidi, N. et al. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol. Syst. Biol. 7, 521 (2011).
Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56–62 (2007).
Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007). In this paper, a synthetic recombinase-based memory device based on stem cell-specific Cre expression and Cre-dependent expression of β-galactosidase is repurposed for lineage tracing and enables the discovery and characterization of adult intestinal stem cells in mice.
Lescroart, F. et al. Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development. Nat. Cell Biol. 16, 829–840 (2014).
Chung, S. et al. Identification of preoptic sleep neurons using retrograde labelling and gene profiling. Nature 545, 477–481 (2017).
Ruegg, T. L. et al. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat. Commun. 5, 3490 (2014).
Minty, J. J. et al. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc. Natl Acad. Sci. USA 110, 14592–14597 (2013).
Chen, Y., Kim, J. K., Hirning, A. J., Josic, K. & Bennett, M. R. Emergent genetic oscillations in a synthetic microbial consortium. Science 349, 986–989 (2015). In this study, the dual-feedback architecture proposed in reference 114 is validated at the intercellular level to create oscillating bacterial populations (termed synthetic consortia), which consist of specialized activator and repressor strains.
Regot, S. et al. Distributed biological computation with multicellular engineered networks. Nature 469, 207–211 (2011).
Auslander, D. et al. Programmable full-adder computations in communicating three-dimensional cell cultures. Nat. Methods 15, 57–60 (2018). This work marks the pinnacle of complexity in the design of prototype gene circuits; synthetic consortia consisting of individual human cell populations transgenic for specific Boolean logic functions are programmed to operate robust full-adder computations of environmental signals.
Kemmer, C. et al. A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms. J. Control. Release 150, 23–29 (2011).
Windbichler, N. et al. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature 473, 212–215 (2011).
Hammond, A. et al. A CRISPR–Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat. Biotechnol. 34, 78–83 (2016).
Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838–4843 (2014).
Riglar, D. T. et al. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat. Biotechnol. 35, 653–658 (2017).
Whitaker, W. R., Shepherd, E. S. & Sonnenburg, J. L. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 169, 538–546.e12 (2017).
Borrero, J., Chen, Y., Dunny, G. M. & Kaznessis, Y. N. Modified lactic acid bacteria detect and inhibit multiresistant enterococci. ACS Synth. Biol. 4, 299–306 (2015).
Wright, C. M., Wright, R. C., Eshleman, J. R. & Ostermeier, M. A protein therapeutic modality founded on molecular regulation. Proc. Natl Acad. Sci. USA 108, 16206–16211 (2011).
Swofford, C. A., Van Dessel, N. & Forbes, N. S. Quorum-sensing Salmonella selectively trigger protein expression within tumors. Proc. Natl Acad. Sci. USA 112, 3457–3462 (2015).
Torikai, H. 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 119, 5697–5705 (2012).
Roybal, K. T. et al. Precision tumor recognition by T cells with combinatorial antigen-sensing circuits. Cell 164, 770–779 (2016).
Roybal, K. T. et al. Engineering T cells with customized therapeutic response programs using synthetic Notch receptors. Cell 167, 419–432.e6 (2016).
Eil, R. et al. Ionic immune suppression within the tumour microenvironment limits T cell effector function. Nature 537, 539–543 (2016).
Moon, E. K. et al. Expression of a functional CCR2 receptor enhances tumor localization and tumor eradication by retargeted human T cells expressing a mesothelin-specific chimeric antibody receptor. Clin. Cancer Res. 17, 4719–4730 (2011).
Wu, C. Y., Roybal, K. T., Puchner, E. M., Onuffer, J. & Lim, W. A. Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. Science 350, aab4077 (2015). In this work, the autonomous tumour recognition and destruction programme of CAR T cells is rendered conditionally activatable by small molecule drugs; initiation of CD3ζ-dependent T cell signalling relies on chemically induced protein dimerization.
Grada, Z. et al. TanCAR: a novel bispecific chimeric antigen receptor for cancer immunotherapy. Mol. Ther. Nucleic Acids 2, e105 (2013).
Fedorov, V. D., Themeli, M. & Sadelain, M. PD-1- and CTLA-4-based inhibitory chimeric antigen receptors (iCARs) divert off-target immunotherapy responses. Sci. Transl Med. 5, 215ra172 (2013).
Xie, M. et al. beta-cell-mimetic designer cells provide closed-loop glycemic control. Science 354, 1296–1301 (2016). This work shows that expression of voltage-gated calcium channels is decisive for glucose sensing in non-endocrine human cell types and indicates that synthetic gene circuits programming human cells for closed-loop control of glucose homeostasis could provide an important alternative to β-cell differentiation (see references 127 and 145) in future cell-based diabetes treatments.
Ye, H. et al. Self-adjusting synthetic gene circuit for correcting insulin resistance. Nat. Biomed. Eng. 1, 0005 (2017).
Schukur, L., Geering, B., Charpin-El Hamri, G. & Fussenegger, M. Implantable synthetic cytokine converter cells with AND-gate logic treat experimental psoriasis. Sci. Transl Med. 7, 318ra201 (2015).
Bai, P. et al. A synthetic biology-based device prevents liver injury in mice. J. Hepatol. 65, 84–94 (2016).
Kemmer, C. et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat. Biotechnol. 28, 355–360 (2010).
Rossger, K., Charpin-El Hamri, G. & Fussenegger, M. Reward-based hypertension control by a synthetic brain-dopamine interface. Proc. Natl Acad. Sci. USA 110, 18150–18155 (2013).
Auslander, D. et al. A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol. Cell 55, 397–408 (2014).
Rossger, K., Charpin-El-Hamri, G. & Fussenegger, M. A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat. Commun. 4, 2825 (2013).
Saxena, P., Charpin-El Hamri, G., Folcher, M., Zulewski, H. & Fussenegger, M. Synthetic gene network restoring endogenous pituitary-thyroid feedback control in experimental Graves’ disease. Proc. Natl Acad. Sci. USA 113, 1244–1249 (2016).
Di Stasi, A. et al. Inducible apoptosis as a safety switch for adoptive cell therapy. N. Engl. J. Med. 365, 1673–1683 (2011).
Chan, C. T., Lee, J. W., Cameron, D. E., Bashor, C. J. & Collins, J. J. ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nat. Chem. Biol. 12, 82–86 (2016).
Shao, J. et al. Smartphone-controlled optogenetically engineered cells enable semiautomatic glucose homeostasis in diabetic mice. Sci. Transl Med. 9, eaal2298 (2017). By integrating software engineering and synthetic biology, the authors of this study create a telemedicine concept for future personalized cell-based diabetes therapy; in their design, smartphone-controlled light-emitting diode (LED) implants regulate the release of insulinogenic hormones by human cells transgenic for red light-inducible gene expression.
Lim, W. A. & June, C. H. The principles of engineering immune cells to treat cancer. Cell 168, 724–740 (2017).
Klebanoff, C. A., Rosenberg, S. A. & Restifo, N. P. Prospects for gene-engineered T cell immunotherapy for solid cancers. Nat. Med. 22, 26–36 (2016).
Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R. & Benenson, Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333, 1307–1311 (2011).
Nissim, L. & Bar-Ziv, R. H. A tunable dual-promoter integrator for targeting of cancer cells. Mol. Syst. Biol. 6, 444 (2010).
Gaber, R. et al. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat. Chem. Biol. 10, 203–208 (2014).
Kramer, B. P., Fischer, C. & Fussenegger, M. BioLogic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 87, 478–484 (2004).
Rinaudo, K. et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25, 795–801 (2007).
Lienert, F. et al. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res. 41, 9967–9975 (2013).
Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C. & Voigt, C. A. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249–253 (2012).
Win, M. N. & Smolke, C. D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456–460 (2008).
Wang, W. et al. A light- and calcium-gated transcription factor for imaging and manipulating activated neurons. Nat. Biotechnol. 35, 864–871 (2017).
Leisner, M., Bleris, L., Lohmueller, J., Xie, Z. & Benenson, Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat. Nanotechnol 5, 666–670 (2010).