hero technology

UNIQUE PLATFORM FOR saRNA DRUG DISCOVERY

RNAa TECHNOLOGY

By utilizing short, non-coding oligonucleotides to specifically target and up-regulate therapeutic genes, RNAa offers the ability to modulate previously undruggable targets. It represents one of the few available technologies that can be translated into the clinic to treat diseases corrected by stimulating the expression of silenced therapeutic genes.

RNAa'S ADVANTAGES

RNAa uses short, non-coding oligonucleotides to target and ‘turn up’ transcription of an endogenous gene leading to restoration of endogenous protein function.  RNAa offers unprecedented advantages:

  1. Expanded disease spaces by targeting nearly any beneficial gene including In theory, any gene could be targeted by RNAa including disease-beneficial genes, instead of disease-causing genes, offering new hope for many diseases undruggable by conventional approaches such as those caused by epigenetic silencing or downregulation of target gene expression.


  2. Faithful restoration of natural gene function.


  3. Persistent expression of target gene.


  4. Pre-established medicinal chemistries and drug delivery platforms developed for gene silencing techniques are readily implemented accelerating in-house drug development.


  5. Our in-house expedited and cost-saving screening process rapidly identifies numerous activating oligonucleotides for targeted genes of choice. Each represents a candidate API.


  6. Additional tweaks improve medicinal properties and maximize transcriptional output for selected lead candidates.

RACTIGEN'S APPROACH

Vector-based systems (e.g., viral, plasmid, etc.) have been the traditional approach to gene therapy. All vector-based systems require large artificial expression constructs that typically do not resemble natural genes. They contain many foreign sequences from viruses or other sources that drive production of modified genes present in the expression construct.  Furthermore, vector-based systems (e.g. viral gene therapies) have been linked to major health problems including secondary malignancies and even death.

On the other hand, small oligonucleotides do not encode for any exogenous genes. Rather, their activity is largely based on principles of complementary base pairing. Over the past decade, oligonucleotides have emerged as an important new class of therapeutic molecules. However, nearly all oligonucleotide-based drugs exhibit only an inhibitory mechanism of action in that they silence gene expression.

Our platform is based on RNAa technology that utilizes short, non-coding oligonucleotides to specifically target and up-regulate therapeutic genes rather than silence them. As a consequence, our pharmaceutical development process benefits from the use of already established medicinal chemistry and drug delivery platforms accelerating drug development. In addition, RNAa has the unique ability to enhance transcription of a targeted gene offering for a more natural alternative to gene therapies, as well as the ability to restore expression of silenced genes previously thought of as undruggable targets.

RNAa TIMELINE

  • 1969

    R. J. Britten and E. H. Davidson proposed the gene-battery model in which activator RNA induces gene expression in the nucleus by binding to gene promoter (Britten and Davidson. Science 1969)

  • 2006

    RNAa discovered  – Li et al. first demonstrated RNAa in human cells and coined the term (Li et al. PNAS 2006)

  • 2007

    Janowski et al. reported RNAa in human cells (Janowski et al. Nature Chem Biol 2007)

  • 2008

    Place et al. reported RNAa induced by miRNA (Place et al. PNAS 2008)

  • 2009

    First in vivo study of RNAa – Turunen et al tested RNAa's therapeutic use in vivo and proposed the concept of epigenetherapy (Turunen et al. Circ Res 2009)

  • 2010

    Huang et al. reported conservation of RNAa in mammalian cells (Huang et al. PLoS One 2010)

  • 2012

    Huang et al. reported miRNA-induced RNAa in physiological context (Huang et al. NAR 2012)

  • 2012

    Long-Cheng Li Lab at UCSF and Alnylam Pharmaceuticals jointly published two preclinical studies of treating prostate and bladder cancer using saRNA (Place et al. Mol Ther-Nucleic Acids 2012; Kang et al. Cancer Res 2013)

  • 2013

    Seth et al. reported RNAa in C. elegans (Seth et al. Dev Cell 2013)

  • 2013

    Turner et al reported miRNA-mediated RNAa in C. elegans (Turner et al. Cell Cycle 2014)

  • 2014

    UK-based MiNA Therapeutics licensed rights of RNAa-related intellectual property created in Long-Cheng Li Lab at UCSF (read the news)  

  • 2016

    The first clinical trial of RNAa-based therapy — The first-ever saRNA drug developed by MiNA Therapeutics entered clinical trial (NIH clinical trial number: NCT02716012)

  • 2016

    Portnoy et al. reported the identification of the RITA (RNA-induced transcriptional activation) complex (Portnoy et al. Cell Res 2016);  Meng et al. published new understanding of RNAa mechanism (Meng et al. Nucleic Acid Res 2016)

Intellectual Property

Ractigen uses a powerful, high-throughput discovery engine to rapidly identify numerous activating oligonucleotides for any single target gene. In combination, we implement a highly refined bioinformatics search engine to identify sequences susceptible to gene activation. Neither process relies on knowledge or function of non-coding RNA transcripts or chromatin structure to identify successful candidates. We are actively generating thousands of oligonucleotides capable of activating an ever-growing list of therapeutic genes to expand our IP estate and actively pushing our lead compound to Phase I clinical trials.

Publications and Presentations

  1. Kang MR, Park KH, Lee CW, Lee MY, Han SB, Li LC, Kang JS. Small activating RNA induced expression of VHL gene in renal cell carcinoma. Int J Biochem Cell Biol. 2018 Feb: S1357-2725(18)30030-X. 
  2. Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC. saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. Cell Res. 2016 Feb 23.
  3. Wang J, Place RF, Portnoy V, Huang V, Kang MR, Kosaka M, Ho MK, Li LC. Inducing gene expression by targeting promoter sequences using small activating RNAs. J Biol Methods. 2015 Mar 11; 2(1).
  4. Wang J, Huang V, Ye L, Bárcena A, Lin G, Lue TF and Li LC. Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. Stem Cell Dev 2014 Sep 18.
  5. Wang X, Wang J, Huang V, Place RF, and Li LC. Induction of NANOG expression by targeting promoter sequence with small activating RNA antagonizes retinoic acid-induced differentiation. Biochem J 2012 May 1; 443(3):821-8.
  6. Wang T, Li M, Yuan H, Zhan Y, Xu H, Wang S, Yang W, Liu J and Li LC. Small activating RNA-guided iNOS up-regulation improves erectile function of diabetic rats. J Urol 2013 Aug; 190(2):790-8.
  7. Kosaka M, Kang MR, Yang G and Li LC. Targeted p21 WAF1/CIP1 activation by RNAa inhibits hepatocellular carcinoma cells. Nucleic Acid Ther 2012 2012 Oct; 22(5):335-43.
  8. Kang MR, Yang G, Place RF, Charisse K, Epstein-Barash H, Manoharan H and LI LC. Intravesical delivery of small activating RNA formulated into lipid nanoparticles inhibits orthotopic bladder tumor growth. Cancer Res 2012 Oct 1;72(19):5069-79.  
  9. Ren S, Kang MR, Wang J, Huang V, Place RF, Sun Y, Li LC. Targeted induction of endogenous NKX3-1 by small activating RNA inhibits prostate tumor growth. Prostate. Oct; 73(14):1591-601.
  10. Place RF, Wang J, Noonan E, Meyers R, Manoharan M, Charisse K, Duncan R, Huang V, Wang X and Li LC. Formulation of small activating RNA into lipidoid nanoparticles inhibits xenograft prostate tumor growth by inducing p21 expression. Molecular Therapy - Nucleic Acids 2012; e15.
  11. Chen Z, Place RF, Jia ZJ, Pookot D, Dahiya R, Li LC. Antitumor effect of dsRNA-induced p21WAF1/CIP1 gene activation in human bladder cancer cells. Mol Cancer Ther. 2008 Mar;7(3):698-703.
  12. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1608-13. Epub 2008 Jan 28.
  13. Li LC, Okino ST, Zhao H, Pokot D, Place RF, Dahiya R. Small double-stranded RNAs induce transcriptional activation in human cells. Proc Natl Acad Sci USA. 2006 Nov 14;103(46):17337-17342.
  1. Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE, Corey DR. Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol. 2007;3:166-73.
  2. Yue X, Schwartz JC, Chu Y, Younger ST, Gagnon KT, Elbashir S, et al. Transcriptional regulation by small RNAs at sequences downstream from 3' gene termini. Nat Chem Biol. 2010;6:621-9.
  3. Turunen MP, Lehtola T, Heinonen SE, Assefa GS, Korpisalo P, Girnary R, et al. Efficient regulation of VEGF expression by promoter-targeted lentiviral shRNAs based on epigenetic mechanism: a novel example of epigenetherapy. Circ Res. 2009;105:604-9.
  4. Turner MJ, Jiao AL, Slack FJ. Autoregulation of lin-4 microRNA transcription by RNA activation (RNAa) in C. elegans. Cell Cycle. 2014;13:772-81.
  5. Chu Y, Yue X, Younger ST, Janowski BA, Corey DR. Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter. Nucleic Acids Res. 2010;38:7736-48.
  6. Meng X, Jiang Q, Chang N, Wang X, Liu C, Xiong J, et al. Small activating RNA binds to the genomic target site in a seed-region-dependent manner. Nucleic Acids Res. 2016;44:2274-82.
  7. Hu J, Chen Z, Xia D, Wu J, Xu H, Ye ZQ. Promoter-associated small double-stranded RNA interacts with heterogeneous nuclear ribonucleoprotein A2/B1 to induce transcriptional activation. Biochem J. 2012;447:407-16.
  8. Chaluvally-Raghavan P, Jeong KJ, Pradeep S, Silva AM, Yu S, Liu W, et al. Direct Upregulation of STAT3 by MicroRNA-551b-3p Deregulates Growth and Metastasis of Ovarian Cancer. Cell Rep. 2016;15:1493-504.
  9. Matsui M, Chu Y, Zhang H, Gagnon KT, Shaikh S, Kuchimanchi S, et al. Promoter RNA links transcriptional regulation of inflammatory pathway genes. Nucleic Acids Res. 2013;41:10086-109.
  10. Matsui M, Sakurai F, Elbashir S, Foster DJ, Manoharan M, Corey DR. Activation of LDL receptor expression by small RNAs complementary to a noncoding transcript that overlaps the LDLR promoter. Chem Biol. 2010;17:1344-55.
  11. Lopez P, Wagner KD, Hofman P, Van Obberghen E. RNA Activation of the Vascular Endothelial Growth Factor Gene (VEGF) Promoter by Double-Stranded RNA and Hypoxia: Role of Noncoding VEGF Promoter Transcripts. Mol Cell Biol. 2016;36:1480-93.
  12. Turunen MP, Husso T, Musthafa H, Laidinen S, Dragneva G, Laham-Karam N, et al. Epigenetic upregulation of endogenous VEGF-A reduces myocardial infarct size in mice. PLoS One. 2014;9:e89979.
  13. Reebye V, Saetrom P, Mintz PJ, Rossi JJ, Kasahara N, Nteliopoulos G, et al. A Short-activating RNA Oligonucleotide Targeting the Islet beta-cell Transcriptional Factor MafA in CD34(+) Cells. Mol Ther Nucleic Acids. 2013;2:e97.
  14. Reebye V, Saetrom P, Mintz PJ, Huang KW, Swiderski P, Peng L, et al. Novel RNA oligonucleotide improves liver function and inhibits liver carcinogenesis in vivo. Hepatology. 2014;59:216-27.
  15. Yoon S, Huang KW, Reebye V, Mintz P, Tien YW, Lai HS, et al. Targeted Delivery of C/EBPalpha -saRNA by Pancreatic Ductal Adenocarcinoma-specific RNA Aptamers Inhibits Tumor Growth In Vivo. Mol Ther. 2016.
  16. Li C, Jiang W, Hu Q, Li LC, Dong L, Chen R, et al. Enhancing DPYSL3 gene expression via a promoter-targeted small activating RNA approach suppresses cancer cell motility and metastasis. Oncotarget. 2016;7:22893-910.
  17. Wang LL, Feng CL, Zheng WS, Huang S, Zhang WX, Wu HN, et al. Tumor-selective lipopolyplex encapsulated small active RNA hampers colorectal cancer growth in vitro and in orthotopic murine. Biomaterials. 2017;141:13-28.
  18. Harris EA, Buzina A, Moffat J, McMillen DR. Design and Experimental Validation of Small Activating RNAs Targeting an Exogenous Promoter in Human Cells. . ACS Synth Biol. 2017 Apr 21;6(4):628-637. doi: 10.1021/acssynbio.6b00125. Epub 2017 Jan 17. PubMed PMID: 28033709.
  19. Voutila J, Reebye V, Roberts TC, Protopapa P, Andrikakou P, Blakey DC, Habib R, Huber H, Saetrom P, Rossi JJ, Habib NA. Development and Mechanism of Small Activating RNA Targeting CEBPA, a Novel Therapeutic in Clinical Trials for Liver Cancer. Mol Ther. 2017 Dec 6;25(12):2705-2714. doi: 10.1016/j.ymthe.2017.07.018. Epub 2017 Aug 4. PubMed PMID: 28882451.
  20. Zhang Y, Liu W, Chen Y, Liu J, Wu K, Su L, Zhang W, Jiang Y, Zhang X, Zhang Y, Liu C, Tao L, Liu B, Zhang H. A Cellular MicroRNA Facilitates Regulatory T Lymphocyte Development by Targeting the FOXP3 Promoter TATA-Box Motif. J Immunol. 2017 Dec 27. pii: ji1700196. doi: 10.4049/jimmunol.1700196. [Epub ahead of print] PubMed PMID: 29282311.
  1. Zeng T, Duan X, Zhu W, Liu Y, Wu W, Zeng G. SaRNA-mediated activation of TRPV5 reduces renal calcium oxalate deposition in rat via decreasing urinary calcium excretion. Urolithiasis. 2017 Aug 3.
  2. Wang LL, Feng CL, Zheng WS, Huang S, Zhang WX, Wu HN, Zhan Y, Han YX, Wu S,Jiang JD. Tumor-selective lipopolyplex encapsulated small active RNA hampers colorectal cancer growth in vitro and in orthotopic murine. Biomaterials. 2017Oct;141:13-28.
  3. Fimiani C, Goina E, Su Q, Gao G, Mallamaci A. RNA activation of haploinsufficient Foxg1 gene in murine neocortex. Sci Rep. 2016 Dec 20;6:39311.
  4. Huan H, Wen X, Chen X, Wu L, Liu W, Habib NA, Bie P, Xia F. C/EBPα Short-Activating RNA Suppresses Metastasis of Hepatocellular Carcinoma through Inhibiting EGFR/β-Catenin Signaling Mediated EMT. PLoS One. 2016 Apr6;11(4):e0153117.  
  5. Li C, Jiang W, Hu Q, Li LC, Dong L, Chen R, Zhang Y, Tang Y, Thrasher JB, Liu CB, Li B. Enhancing DPYSL3 gene expression via a promoter-targeted small activating RNA approach suppresses cancer cell motility and metastasis. Oncotarget. 2016 Apr 19;7(16):22893-910.  
  6. Wang C, Ge Q, Zhang Q, Chen Z, Hu J, Li F, Ye Z. Targeted p53 activation by saRNA suppresses human bladder cancer cells growth and metastasis. J Exp Clin Cancer Res. 2016 Mar 25;35:53.  
  7. Yoon S, Huang KW, Reebye V, Mintz P, Tien YW, Lai HS, Sætrom P, Reccia I, Swiderski P, Armstrong B, Jozwiak A, Spalding D, Jiao L, Habib N, Rossi JJ. Targeted Delivery of C/EBPα -saRNA by Pancreatic Ductal Adenocarcinoma-specific RNA Aptamers Inhibits Tumor Growth In Vivo. Mol Ther. 2016 Jun;24(6):1106-1116.
  8. Turunen MP, Husso T, Musthafa H, Laidinen S, Dragneva G, Laham-Karam N, Honkanen S, Paakinaho A, Laakkonen JP, Gao E, Vihinen-Ranta M, Liimatainen T, Ylä-Herttuala S. Epigenetic upregulation of endogenous VEGF-A reduces myocardial infarct size in mice. PLoS One. 2014 Feb 26;9(2):e89979.
  9. Ren S, Kang MR, Wang J, Huang V, Place RF, Sun Y, Li LC. Targeted induction of endogenous NKX3-1 by small activating RNA inhibits prostate tumor growth. Prostate. 2013 Oct;73(14):1591-601.  
  10. Wang T, Li M, Yuan H, Zhan Y, Xu H, Wang S, Yang W, Liu J, Ye Z, Li LC. saRNA guided iNOS up-regulation improves erectile function of diabetic rats. J Urol.2013 Aug;190(2):790-8.
  11. Zhang Z, Wang Z, Liu X, Wang J, Li F, Li C, Shan B. Up-regulation of p21WAF1/CIP1 by small activating RNA inhibits the in vitro and in vivo growth of pancreatic cancer cells. Tumori. 2012 Nov;98(6):804-11.
  12. Place RF, Wang J, Noonan EJ, Meyers R, Manoharan M, Charisse K, Duncan R, Huang V, Wang X, Li LC. Formulation of Small Activating RNA Into Lipidoid Nanoparticles Inhibits Xenograft Prostate Tumor Growth by Inducing p21Expression. Mol Ther Nucleic Acids. 2012 Mar 27;1:e15.
  13. Kang MR, Yang G, Place RF, Charisse K, Epstein-Barash H, Manoharan M, Li LC. Intravesical delivery of small activating RNA formulated into lipid nanoparticles inhibits orthotopic bladder tumor growth. Cancer Res. 2012 Oct 1;72(19):5069-79.
  14. Turunen MP, Lehtola T, Heinonen SE, Assefa GS, Korpisalo P, Girnary R, Glass CK, Väisänen S, Ylä-Herttuala S. Efficient regulation of VEGF expression by promoter-targeted lentiviral shRNAs based on epigenetic mechanism: a novel example of epigenetherapy. Circ Res. 2009 Sep 11;105(6):604-9.

Reviews

  1. Li LC. Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells. Adv Exp Med Biol. 2017;983:1-20.
  2. Kang MR, Li G, Pan T, Xing JC, Li LC. Development of therapeutic dsP21-322 for Cancer Treatment. Adv Exp Med Biol. 2017;983:217-229.
  3. Corey DR. RNA-Mediated Gene Activation: Identifying a Candidate RNA for Preclinical Development.Adv Exp Med Biol. 2017;983:161-171.
  4. Mallamaci A. Enhancing Neuronogenesis and Counteracting Neuropathogenic Gene Haploinsufficiencies by RNA Gene Activation. Adv Exp Med Biol. 2017;983:23-39.
  5. Vaschetto LM. RNA Activation: A Diamond in the Rough for Genome Engineers. J Cell Biochem. 2017 Jun 21.
  6. Gustincich S, Zucchelli S, Mallamaci A. The Yin and Yang of nucleic acid-based therapy in the brain. Prog Neurobiol. 2017 Aug;155:194-211.
  7. Guo D, Barry L, Lin SS, Huang V, Li LC. RNAa in action: from the exception to the norm. RNA Biol. 2014;11(10):1221-5.
  8. Zheng L, Wang L, Gan J, Zhang H. RNA activation: promise as a new weapon against cancer. Cancer Lett. 2014 Dec 1;355(1):18-24.
  9. Jiao AL, Slack FJ. RNA-mediated gene activation. Epigenetics. 2014 Jan;9(1):27-36.
  10. Esquela-Kerscher A. The lin-4 microRNA: The ultimate micromanager. Cell Cycle. 2014;13(7):1060-1.
  11. Li LC. Chromatin remodeling by the small RNA machinery in mammalian cells. Epigenetics. 2014 Jan;9(1):45-52.
  12. Portnoy V, Huang V, Place RF, Li LC. Small RNA and transcriptional upregulation. Wiley Interdiscip Rev RNA. 2011 Sep-Oct;2(5):748-60.
  13. Janowski BA, Corey DR. Minireview: Switching on progesterone receptor expression with duplex RNA. Mol Endocrinol. 2010 Dec;24(12):2243-52.
  14. Pushparaj PN, Aarthi JJ, Kumar SD, Manikandan J. RNAi and RNAa--the yin and yang of RNAome. Bioinformation. 2008 Jan 11;2(6):235-7.
  15. Rossi JJ. Transcriptional activation by small RNA duplexes.Nature Chem Biol 2007 March;3(3):136-37.

News & Commentaries

  1. Garber K. Small RNAs reveal an activating side. Science 2006 Nov 3;313:741-42.
  2. How to get your genes switched on. New Scientist 2006 Nov 18:20.
  3. Elizabeth M. Activating gene expression. Science. STKE 2006 Nov 21;362:392.
  4. Karberg S. Positive Interferenz. Süddeutsche Zeitung 2006 Nov 8.
  5. Holmes B. Switched on. New Scientist 2007 April 7:42-45.
  6. Okoye SE. Scientists' new genes discovery may be manipulated to disable any disease. Guardian 2007 Jul 5.
  7. Check E. Hitting the on switch. Nature 2007 Aug 23;448:885-58.
  8. Dolgin E. Now showing: RNA Activation. The Scientist 2009;23(5):34-39.
  9. Payton S. Intravesical RNA activation—a new treatment concept. Nature Reviews Urol 2012 August 28.
  10. Oligonucleotide Therapeutics Society. Perspectives on current science – June 2016.