Design and mathematical analysis of activating transcriptional amplifiers that enable modular temporal control in synthetic juxtacrine circuits

Synthetic and Systems Biotechnology - Tập 8 - Trang 654-672 - 2023
Calvin Lam

Tài liệu tham khảo

Santorelli, 2019, Synthetic development: building mammalian multicellular structures with artificial genetic programs, Curr Opin Biotechnol, 59, 130, 10.1016/j.copbio.2019.03.016 Lam, 2022, Synthetic immunotherapy: programming immune cells with novel and sophisticated logic capabilities, Transplant Cell Ther, 28, 560, 10.1016/j.jtct.2022.06.001 Roybal, 2017, Synthetic immunology: hacking immune cells to expand their therapeutic capabilities, Annu Rev Immunol, 35, 229, 10.1146/annurev-immunol-051116-052302 McNamara, 2023, Synthetic developmental biology: new tools to deconstruct and rebuild developmental systems, Semin Cell Dev Biol, 141, 33, 10.1016/j.semcdb.2022.04.013 Ho, 2021, Novel synthetic biology approaches for developmental systems, Stem Cell Rep, 16, 1051, 10.1016/j.stemcr.2021.04.007 Martínez-Ara, 2022, Scaling up complexity in synthetic developmental biology, Science (1979), 378, 864 Kim, 2020, Engineering and modeling of multicellular morphologies and patterns, Curr Opin Genet Dev, 63, 95, 10.1016/j.gde.2020.05.039 Toda, 2019, Engineering cell–cell communication networks: programming multicellular behaviors, Curr Opin Chem Biol, 52, 31, 10.1016/j.cbpa.2019.04.020 Toda, 2018, Programming self-organizing multicellular structures with synthetic cell-cell signaling, Science (1979), 361, 156 Lim, 2017, The principles of engineering immune cells to treat cancer, Cell, 168, 724, 10.1016/j.cell.2017.01.016 Choe, 2020, Engineering T cells to treat cancer: the convergence of immuno-oncology and synthetic biology, Annu Rev Cell Biol, 4, 121, 10.1146/annurev-cancerbio-030419-033657 Caliendo, 2019, Engineered cell-based therapeutics: synthetic biology meets immunology, Front Bioeng Biotechnol, 7, 10.3389/fbioe.2019.00043 Azimi, 2019, NextGen cell-based immunotherapies in cancer and other immune disorders, Curr Opin Immunol, 59, 79, 10.1016/j.coi.2019.03.007 Zhang, 2022, Synthetic biology in chimeric antigen receptor T (CAR T) cell engineering, ACS Synth Biol, 11, 1, 10.1021/acssynbio.1c00256 Williams, 2020, Precise T cell recognition programs designed by transcriptionally linking multiple receptors, Science (1979), 370, 1099 Roybal, 2016, Precision tumor recognition by T cells with combinatorial antigen-sensing circuits, Cell, 164, 770, 10.1016/j.cell.2016.01.011 Zhu, 2022, Modular design of synthetic receptors for programmed gene regulation in cell therapies, Cell, 185, 1431, 10.1016/j.cell.2022.03.023 Roybal, 2016, Engineering T cells with customized therapeutic response programs using synthetic notch receptors, Cell, 167, 419, 10.1016/j.cell.2016.09.011 Morsut, 2016, Engineering customized cell sensing and response behaviors using synthetic notch receptors, Cell, 164, 780, 10.1016/j.cell.2016.01.012 Toda, 2020, Engineering synthetic morphogen systems that can program multicellular patterning, Science (1979), 370, 327 Choe, 2021, SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma, Sci Transl Med, 13, 10.1126/scitranslmed.abe7378 Yang, 2020, Engineering of an enhanced synthetic Notch receptor by reducing ligand-independent activation, Commun Biol, 3, 116, 10.1038/s42003-020-0848-x Saga, 2012, The mechanism of somite formation in mice, Curr Opin Genet Dev, 22, 331, 10.1016/j.gde.2012.05.004 Goldbeter, 2008, Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways, J Theor Biol, 252, 574, 10.1016/j.jtbi.2008.01.006 Miao, 2022, Reconstruction and deconstruction of human somitogenesis in vitro, Nature Hester, 2011, A multi-cell, multi-scale model of vertebrate segmentation and somite formation, PLoS Comput Biol, 7, 10.1371/journal.pcbi.1002155 Pan, 2006, A negative feedback loop of transcription factors that controls stem cell pluripotency and self‐renewal, Faseb J, 20, 1730, 10.1096/fj.05-5543fje Su, 2015, IL-2Rα mediates temporal regulation of IL-2 signaling and enhances immunotherapy, Sci Transl Med, 7, 10.1126/scitranslmed.aac8155 Sato, 1998, Positive feedback regulation of type I IFN genes by the IFN-inducible transcription factor IRF-7, FEBS Lett, 441, 106, 10.1016/S0014-5793(98)01514-2 Huang, 2015, Temporal control of plant organ growth by TCP transcription factors, Curr Biol, 25, 1765, 10.1016/j.cub.2015.05.024 Feldker, 2020, Genome-wide cooperation of EMT transcription factor ZEB1 with YAP and AP-1 in breast cancer, EMBO J, 39, 10.15252/embj.2019103209 Burrill, 2012, Synthetic memory circuits for tracking human cell fate, Genes Dev, 26, 1486, 10.1101/gad.189035.112 Lam, 2022, Parameterized computational framework for the description and design of genetic circuits of morphogenesis based on contact-dependent signaling and changes in cell–cell adhesion, ACS Synth Biol, 11, 1417, 10.1021/acssynbio.0c00369 Swat, 2012, Chapter 13 - multi-scale modeling of tissues using CompuCell3D, 110 325 Lam, 2022, Parameterized computational framework for the description and design of genetic circuits of morphogenesis based on contact-dependent signaling and changes in cell–cell adhesion, ACS Synth Biol, 11, 1417, 10.1021/acssynbio.0c00369 Allen, 2023, Synthetic cytokine circuits that drive T cells into immune-excluded tumors, Science (1979), 378 Hyrenius-Wittsten, 2021, SynNotch CAR circuits enhance solid tumor recognition and promote persistent antitumor activity in mouse models, Sci Transl Med, 13, 10.1126/scitranslmed.abd8836 Shaya, 2017, Cell-cell contact area affects notch signaling and notch-dependent patterning, Dev Cell, 40, 505, 10.1016/j.devcel.2017.02.009 Allen, 2022, Rethinking cancer targeting strategies in the era of smart cell therapeutics, Nat Rev Cancer, 22, 693, 10.1038/s41568-022-00505-x Dufva, 2020, Integrated drug profiling and CRISPR screening identify essential pathways for CAR T-cell cytotoxicity, Blood, 135, 597, 10.1182/blood.2019002121 Singh, 2020, Impaired death receptor signaling in leukemia causes antigen-independent resistance by inducing CAR T-cell dysfunction, Cancer Discov, 10, 552, 10.1158/2159-8290.CD-19-0813 Lemoine, 2021, Overcoming intrinsic resistance of cancer cells to CAR T-cell killing, Clin Cancer Res, 27, 6298, 10.1158/1078-0432.CCR-21-1559 Hernandez-Lopez, 2021, T cell circuits that sense antigen density with an ultrasensitive threshold, Science (1979), 371, 1166 Wu, 2015, Remote control of therapeutic T cells through a small molecule–gated chimeric receptor, Science (1979), 350 O'Donoghue, 2021, T cells selectively filter oscillatory signals on the minutes timescale, Proc Natl Acad Sci USA, 118 Drent, 2018, Feasibility of controlling CD38-CAR T cell activity with a Tet-on inducible CAR design, PLoS One, 13, 10.1371/journal.pone.0197349 Walker, 2017, Tumor antigen and receptor densities regulate efficacy of a chimeric antigen receptor targeting anaplastic lymphoma kinase, Mol Ther, 25, 2189, 10.1016/j.ymthe.2017.06.008 Majzner, 2019, CAR T cells targeting B7-H3, a pan-cancer antigen, demonstrate potent preclinical activity against pediatric solid tumors and brain tumors, Clin Cancer Res, 25, 2560, 10.1158/1078-0432.CCR-18-0432 Lemoine, 2021, Born to survive: how cancer cells resist CAR T cell therapy, J Hematol Oncol, 14, 199, 10.1186/s13045-021-01209-9 Grupp, 2013, Chimeric antigen receptor–modified T cells for acute lymphoid leukemia, N Engl J Med, 368, 1509, 10.1056/NEJMoa1215134 Chen, 2023, Characterization of leukemic resistance to CD19-targeted CAR T-cell therapy through deep genomic sequencing, Cancer Immunol Res, 11, 13, 10.1158/2326-6066.CIR-22-0095 Srivastava, 2015, Engineering CAR-T cells: design concepts, Trends Immunol, 36, 494, 10.1016/j.it.2015.06.004 Salinas, 2020, Potential of glioblastoma-targeted chimeric antigen receptor (CAR) T-cell therapy, CNS Drugs, 34, 127, 10.1007/s40263-019-00687-3 Majzner, 2018, Tumor antigen escape from CAR T-cell therapy, Cancer Discov, 8, 1219, 10.1158/2159-8290.CD-18-0442 O'Rourke, 2017, A single dose of peripherally infused EGFRvIII-directed CAR T cells mediates antigen loss and induces adaptive resistance in patients with recurrent glioblastoma, Sci Transl Med, 9 Song, 2016, Effective adoptive immunotherapy of triple-negative breast cancer by folate receptor-alpha redirected CAR T cells is influenced by surface antigen expression level, J Hematol Oncol, 9, 56, 10.1186/s13045-016-0285-y Prybutok, 2022, Mapping CAR T-cell design space using agent-based models, Front Mol Biosci, 9, 10.3389/fmolb.2022.849363 Zhang, 2022, A computational model of cytokine release syndrome during CAR T-cell therapy, Adv Ther, 5 Liu, 2022, Computational model of CAR T-cell immunotherapy dissects and predicts leukemia patient responses at remission, resistance, and relapse, J Immunother Cancer, 10, 10.1136/jitc-2022-005360 Fischel, 2021, Computational modeling of chimeric antigen receptor (CAR) T-cell therapy of a binary model of antigen receptors in breast cancer, 3267 Rohrs, 2019, Understanding the dynamics of T-cell activation in health and disease through the lens of computational modeling, JCO Clin Cancer Inform, 1, 10.1200/CCI.18.00057 Lienert, 2014, Synthetic biology in mammalian cells: next generation research tools and therapeutics, Nat Rev Mol Cell Biol, 15, 95, 10.1038/nrm3738 Ajo-Franklin, 2007, Rational design of memory in eukaryotic cells, Genes Dev, 21, 2271, 10.1101/gad.1586107 Becskei, 2001, Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion, EMBO J, 20, 2528, 10.1093/emboj/20.10.2528 To, 2010, Noise can induce bimodality in positive transcriptional feedback loops without bistability, Science (1979), 327, 1142 Haynes, 2011, Synthetic reversal of epigenetic silencing, J Biol Chem, 286, 27176, 10.1074/jbc.C111.229567 Cabrera, 2022, The sound of silence: transgene silencing in mammalian cell engineering, Cell Syst, 13, 950, 10.1016/j.cels.2022.11.005 Hartfield, 2017, Multiplexing engineered receptors for multiparametric evaluation of environmental ligands, ACS Synth Biol, 6, 2042, 10.1021/acssynbio.6b00279 Zhou, 2023, Engineering a modular double-transmembrane synthetic receptor system for customizing cellular programs, Cell Rep, 42, 10.1016/j.celrep.2023.112385 Chen, 2021, Programmable protein circuit design, Cell, 184, 2284, 10.1016/j.cell.2021.03.007 Javdan, 2021, Design and development of engineered receptors for cell and tissue engineering, Curr Opin Struct Biol, 28 Barnea, 2008, The genetic design of signaling cascades to record receptor activation, Proc Natl Acad Sci USA, 105, 64, 10.1073/pnas.0710487105 Daringer, 2014, Modular extracellular sensor architecture for engineering mammalian cell-based devices, ACS Synth Biol, 3, 892, 10.1021/sb400128g Schwarz, 2017, Rewiring human cellular input–output using modular extracellular sensors, Nat Chem Biol, 13, 202, 10.1038/nchembio.2253 Pistikou, 2023, Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells, bioRxiv Kipniss, 2017, Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system, Nat Commun, 8, 2212, 10.1038/s41467-017-02075-1 Edelstein, 2020, Elucidation and refinement of synthetic receptor mechanisms, Synth Biol, 5, ysaa017, 10.1093/synbio/ysaa017 Albinger, 2021, Current status and perspective of CAR-T and CAR-NK cell therapy trials in Germany, Gene Ther, 28, 513, 10.1038/s41434-021-00246-w Klichinsky, 2020, Human chimeric antigen receptor macrophages for cancer immunotherapy, Nat Biotechnol, 38, 947, 10.1038/s41587-020-0462-y Gumbiner, 1996, Cell adhesion: the molecular basis of tissue architecture and morphogenesis, Cell, 84, 345, 10.1016/S0092-8674(00)81279-9 Takeichi, 2011, Self-organization of animal tissues: cadherin-mediated processes, Dev Cell, 21, 24, 10.1016/j.devcel.2011.06.002 Alberts, 2002 Persson, 2010 Reeve, 2013, Pharmacodynamic models: parameterizing the Hill equation, michaelis-menten, the logistic curve, and relationships among these models, J Biopharm Stat, 23, 648, 10.1080/10543406.2012.756496 Zhu, 2023, Synthetic multistability in mammalian cells, Science (1979), 375 Barlow, 1989, Hill coefficients and the logistic equation, Trends Pharmacol Sci, 10, 440, 10.1016/S0165-6147(89)80006-9 Prinz, 2010, Hill coefficients, dose–response curves and allosteric mechanisms, J Chem Biol, 3, 37, 10.1007/s12154-009-0029-3 Hutson, 2017, Computational model of secondary palate fusion and disruption, Chem Res Toxicol, 30, 965, 10.1021/acs.chemrestox.6b00350 Anderson, 2005, A hybrid mathematical model of solid tumour invasion: the importance of cell adhesion, Math Med Biol, 22, 163, 10.1093/imammb/dqi005 Dogu, 2009, Mathematical model of a network of interaction between p53 and Bcl-2 during genotoxic-induced apoptosis, Biophys Chem, 143, 44, 10.1016/j.bpc.2009.03.012 McKenna, 2021, BAX and SMAC regulate bistable properties of the apoptotic caspase system, Sci Rep, 11, 3272, 10.1038/s41598-021-82215-2 Ho, 2010, Bistability in apoptosis by receptor clustering, PLoS Comput Biol, 6, 10.1371/journal.pcbi.1000956 MacLachlan, 2002, Apoptotic threshold is lowered by p53 transactivation of caspase-6, Proc Natl Acad Sci USA, 99, 9492, 10.1073/pnas.132241599 Legewie, 2006, Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability, PLoS Comput Biol, 2, e120, 10.1371/journal.pcbi.0020120 Kracikova, 2013, A threshold mechanism mediates p53 cell fate decision between growth arrest and apoptosis, Cell Death Differ, 20, 576, 10.1038/cdd.2012.155