Synthesizing artificial devices that redirect cellular information at will

Natural signaling circuits could be rewired to reprogram cells with pre-determined procedures. However, it is difficult to link cellular signals at will. Here, we describe signal-connectors—a series of RNA devices—that connect one signal to another signal at the translational level. We use them to either repress or enhance the translation of target genes in response to signals. Application of these devices allows us to construct various logic gates and to incorporate feedback loops into gene networks. They have also been used to rewire a native signaling pathway and even to create novel pathways. Furthermore, logical AND gates based on these devices and integration of multiple signals have been used successfully for identification and redirection of the state of cancer cells. Eventually, the malignant phenotypes of cancers have been reversed by rewiring the oncogenic signaling from promoting to suppressing tumorigenesis. We provide a novel platform for redirecting cellular information.

[1]  Timothy K Lu,et al.  Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.

[2]  Travis S. Bayer,et al.  Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.

[3]  L. J. Maher,et al.  Selection and characterization of anti-NF-kappaB p65 RNA aptamers. , 2008, RNA.

[4]  Michael Müller,et al.  Thermodynamic characterization of an engineered tetracycline-binding riboswitch , 2006, Nucleic acids research.

[5]  Piero Carninci,et al.  Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat , 2012, Nature.

[6]  Riccardo Bartoletti,et al.  Molecular Genetic Alterations of c-myc Oncogene in Superficial and Locally Advanced Bladder Cancer , 1998, European Urology.

[7]  C. Buchrieser,et al.  A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes , 2009, Cell.

[8]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[9]  Christina D Smolke,et al.  Synthetic RNA switches as a tool for temporal and spatial control over gene expression. , 2012, Current opinion in biotechnology.

[10]  Howard C. Berg,et al.  Adaptation at the output of the chemotaxis signalling pathway , 2012, Nature.

[11]  Yunde Zhao,et al.  Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. , 2014, Journal of integrative plant biology.

[12]  N. Ferrara,et al.  The biology of VEGF and its receptors , 2003, Nature Medicine.

[13]  M. Wirth,et al.  Simultaneous siRNA-mediated knockdown of antiapoptotic BCL2, Bcl-xL, XIAP and survivin in bladder cancer cells , 2012, International journal of oncology.

[14]  A. Pardi,et al.  High-resolution molecular discrimination by RNA. , 1994, Science.

[15]  L. Serrano,et al.  Engineering Signal Transduction Pathways , 2010, Cell.

[16]  D. Guyer,et al.  Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease , 2006, Nature Reviews Drug Discovery.

[17]  Gautam Sethi,et al.  NF-κB in cancer therapy , 2015, Archives of Toxicology.

[18]  Takashi Ohtsu,et al.  RNA aptamers to mammalian initiation factor 4G inhibit cap-dependent translation by blocking the formation of initiation factor complexes. , 2006, RNA.

[19]  M. Win,et al.  A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2007, Proceedings of the National Academy of Sciences.

[20]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[21]  R. Kong,et al.  SP1-induced upregulation of the long noncoding RNA TINCR regulates cell proliferation and apoptosis by affecting KLF2 mRNA stability in gastric cancer , 2015, Oncogene.

[22]  M. Moore From Birth to Death: The Complex Lives of Eukaryotic mRNAs , 2005, Science.

[23]  A. Sparks,et al.  Identification of c-MYC as a target of the APC pathway. , 1998, Science.

[24]  K. Griendling,et al.  Hydrogen Peroxide Regulates Osteopontin Expression through Activation of Transcriptional and Translational Pathways* , 2013, The Journal of Biological Chemistry.

[25]  Chase L. Beisel,et al.  Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing , 2010, Nucleic acids research.

[26]  Simon Ausländer,et al.  A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. , 2010, Molecular bioSystems.

[27]  Christina D Smolke,et al.  Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins , 2010, Science.

[28]  M. Green,et al.  Controlling gene expression in living cells through small molecule-RNA interactions. , 1998, Science.

[29]  David S. Weiss,et al.  Cas9-mediated targeting of viral RNA in eukaryotic cells , 2015, Proceedings of the National Academy of Sciences.

[30]  R. Breaker,et al.  Riboswitches as antibacterial drug targets , 2006, Nature Biotechnology.

[31]  Yaakov Benenson,et al.  Model‐guided combinatorial optimization of complex synthetic gene networks , 2016, Molecular systems biology.

[32]  Tilman Flock,et al.  Controlling entropy to tune the functions of intrinsically disordered regions. , 2014, Current opinion in structural biology.

[33]  B. Sullenger,et al.  RNA aptamer blockade of osteopontin inhibits growth and metastasis of MDA-MB231 breast cancer cells. , 2009, Molecular therapy : the journal of the American Society of Gene Therapy.

[34]  Jennifer A. Doudna,et al.  Programmable RNA Tracking in Live Cells with CRISPR/Cas9 , 2016, Cell.

[35]  Christopher A. Voigt,et al.  Genetic programs constructed from layered logic gates in single cells , 2012, Nature.

[36]  Xiaoqiang Guo,et al.  Directing cellular information flow via CRISPR signal conductors , 2016, Nature Methods.

[37]  Hong Zhang,et al.  Synthetic circuits, devices and modules , 2010, Protein & Cell.

[38]  Howard J. Li,et al.  Rapid and tunable post-translational coupling of genetic circuits , 2014, Nature.

[39]  Pascale Cossart,et al.  A riboswitch-regulated antisense RNA in Listeria monocytogenes , 2013, Proceedings of the National Academy of Sciences.

[40]  J. Collins,et al.  Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.

[41]  M. Yutsudo,et al.  Cloning of human telomerase catalytic subunit (hTERT) gene promoter and identification of proximal core promoter sequences essential for transcriptional activation in immortalized and cancer cells. , 1999, Cancer research.

[42]  Markus Wieland,et al.  Programmable single-cell mammalian biocomputers , 2012, Nature.