Highly inefficient transit of oligonucleotides from outside cells to the intracellular compartments where functional activity of oligonucleotides takes place is the most serious limitation to practical realization of a full potential of oligonucleotid-based therapies. Several classes of oligonucleotides therapeutics (ONT), including antisense oligonucleotides (ASO), hydrophobically modified siRNAs (hsiRNA), GalNAc conjugated siRNAs, and LNP formulated siRNAs have validated biological efficacy and are in clinic [1, 2]. In all cases, the fraction of oligonucleotides reaching the intended place of biological function is surprisingly low with the majority of molecules being trapped in wrong cellular compartments, resulting in low efficiency and clinically limiting toxicity. Concurrently, there is a significant nd rapidly expanding body of evidence demonstrating natural small RNA trafficking between cells as a means of intracellular communication. Given the extremely high efficacy of oligonucleotide-mediated gene silencing (25-100 molecules of Ago2 loaded siRNAs per cell [3]), exploiting the natural pathways of intracellular small RNA trafficking opens a possibility to dramatically improve the efficacy of ONTs. We hypothesize that exploiting natural, evolutionarily conserved mechanisms and pathways for trafficking of small RNAs across cellular boundaries is the way to fundamentally improve ONTs efficiency. The goal of this proposal is to elucidate the pathways and mechanisms involved in natural small RNA and ONTs trafficking and leverage this knowledge to increase the efficacy of oligonucleotide therapies. We have developed a unique set of experimental tools and analytical methods which enable us to systematically map and study endogenous small RNA as well as ONTs trafficking pathways. We have developed (1) a novel class of hydrophobic siRNAs (hsiRNAs), which efficiently enter cells and tissues;(2) an approach for visualization of native RNA trafficking through use of hsiRNA loaded exosomes as a model, (3) an approach for dissection of productive and non-productive ONTs trafficking using a panel of small molecules dramatically enhancing hsiRNAs efficacy by altering their cellular distribution;(4) a panel of four major classes of ONTs, which utilize different uptake mechanisms and silence a clinically relevant target huntingtin (htt), (5) a panel of engineered cell lines (GFP-fusions of trafficking markers) to study internalization pathways. Using these novel experimental tools along with TESM intracellular imaging, high resolution mass spectrometry and functional and biochemical analyses, we will identify the productive and non-productive cellular uptake mechanisms for both natural and synthetic oligonucleotides Completion of this project will result in (1) significant progress in our understanding of the natural mechanisms of extracellular uptake of small regulatory RNAs, (2) mapping uptake pathways for different classes of ONTs (3) development of the conceptual framework for generation of novel RNA chemistries relying on native uptake mechanisms. These findings will lead to a new generation of ONTs with dramatically improved clinical efficacy.

Public Health Relevance

Oligonucleotide therapeutics has a great promise in the treatment of human diseases. A major limitation of the current clinical applications of oligonucleotide therapies is a low efficiency of their delivery to the functional compartments of the targeted cells. Exploiting the natural mechanisms of small RNA trafficking between cells provides a solution to increase the efficacy of oligonucleotide therapeutics. To utilize natural mechanisms of RNA trafficking and fully realize the promise of oligonucleotide therapies we require a significantly better understanding of the fundamental pathways and molecular mechanisms underlying trafficking of both therapeutic oligonucleotides and natural small RNAs within and between cells. This project will identify these cellular pathways and use this new knowledge for the rational design of the next generation of oligonucleotide therapeutics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM108803-01A1
Application #
8761471
Study Section
Therapeutic Approaches to Genetic Diseases (TAG)
Program Officer
Bender, Michael T
Project Start
2014-08-15
Project End
2018-07-31
Budget Start
2014-08-15
Budget End
2015-07-31
Support Year
1
Fiscal Year
2014
Total Cost
$464,548
Indirect Cost
$187,206
Name
University of Massachusetts Medical School Worcester
Department
Type
Organized Research Units
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
Biscans, Annabelle; Haraszti, Reka A; Echeverria, Dimas et al. (2018) Hydrophobicity of Lipid-Conjugated siRNAs Predicts Productive Loading to Small Extracellular Vesicles. Mol Ther 26:1520-1528
Osborn, Maire F; Coles, Andrew H; Golebiowski, Diane et al. (2018) Efficient Gene Silencing in Brain Tumors with Hydrophobically Modified siRNAs. Mol Cancer Ther 17:1251-1258
Hassler, Matthew R; Turanov, Anton A; Alterman, Julia F et al. (2018) Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo. Nucleic Acids Res 46:2185-2196
Stoddard, Barry L; Khvorova, Anastasia; Corey, David R et al. (2018) Editorial: Nucleic Acids Research and Nucleic Acid Therapeutics. Nucleic Acids Res 46:1563-1564
Ly, Socheata; Navaroli, Deanna M; Didiot, Marie-C├ęcile et al. (2017) Visualization of self-delivering hydrophobically modified siRNA cellular internalization. Nucleic Acids Res 45:15-25
Haraszti, Reka A; Coles, Andrew; Aronin, Neil et al. (2017) Loading of Extracellular Vesicles with Chemically Stabilized Hydrophobic siRNAs for the Treatment of Disease in the Central Nervous System. Bio Protoc 7:
Haraszti, Reka A; Roux, Loic; Coles, Andrew H et al. (2017) 5?-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res 45:7581-7592
Nikan, Mehran; Osborn, Maire F; Coles, Andrew H et al. (2017) Synthesis and Evaluation of Parenchymal Retention and Efficacy of a Metabolically Stable O-Phosphocholine-N-docosahexaenoyl-l-serine siRNA Conjugate in Mouse Brain. Bioconjug Chem 28:1758-1766
Khvorova, Anastasia (2017) Oligonucleotide Therapeutics - A New Class of Cholesterol-Lowering Drugs. N Engl J Med 376:4-7
Godinho, Bruno M D C; Gilbert, James W; Haraszti, Reka A et al. (2017) Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay. Nucleic Acid Ther 27:323-334

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