1
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Gilbert JW, Kennedy Z, Godinho BMDC, Summers A, Weiss A, Echeverria D, Bramato B, McHugh N, Cooper D, Yamada K, Hassler M, Tran H, Gao FB, Brown RH, Khvorova A. Identification of selective and non-selective C9ORF72 targeting in vivo active siRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102291. [PMID: 39233852 PMCID: PMC11372813 DOI: 10.1016/j.omtn.2024.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/29/2024] [Indexed: 09/06/2024]
Abstract
A hexanucleotide (G4C2) repeat expansion (HRE) within intron one of C9ORF72 is the leading genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9ORF72 haploinsufficiency, formation of RNA foci, and production of dipeptide repeat (DPR) proteins have been proposed as mechanisms of disease. Here, we report the first example of disease-modifying siRNAs for C9ORF72 driven ALS/FTD. Using a combination of reporter assay and primary cortical neurons derived from a C9-ALS/FTD mouse model, we screened a panel of more than 150 fully chemically stabilized siRNAs targeting different C9ORF72 transcriptional variants. We demonstrate the lack of correlation between siRNA efficacy in reporter assay versus native environment; repeat-containing C9ORF72 mRNA variants are found to preferentially localize to the nucleus, and thus C9ORF72 mRNA accessibility and intracellular localization have a dominant impact on functional RNAi. Using a C9-ALS/FTD mouse model, we demonstrate that divalent siRNAs targeting C9ORF72 mRNA variants specifically or non-selectively reduce the expression of C9ORF72 mRNA and significantly reduce DPR proteins. Interestingly, siRNA silencing all C9ORF72 mRNA transcripts was more effective in removing intranuclear mRNA aggregates than targeting only HRE-containing C9ORF72 mRNA transcripts. Combined, these data support RNAi-based degradation of C9ORF72 as a potential therapeutic paradigm.
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Affiliation(s)
| | | | | | | | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | | | | | | | - David Cooper
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | - Ken Yamada
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | | | - Hélène Tran
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Fen Biao Gao
- RNA Therapeutic Institute, Worcester, MA 01655, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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2
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Rivera Flores IV, Monopoli K, Jackson S, Echeverria D, O'Reilly D, Brown RH, Khvorova A. Near Sequence Homology Does Not Guarantee siRNA Cross-Species Efficacy. Nucleic Acid Ther 2024. [PMID: 39189114 DOI: 10.1089/nat.2024.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Abstract
Small interfering RNAs (siRNAs) represent a novel class of drugs capable of potent and sustained modulation of genes across various tissues. Preclinical development of siRNAs necessitates assessing efficacy and toxicity in animal models. While identifying therapeutic leads with cross-species activity can expedite development, it may compromise efficacy and be infeasible for certain gene targets. Here, we investigate whether deriving species-active siRNAs from potent human-targeting leads-an approach termed mismatch conversion-can yield potent compounds. We systematically altered potent siRNAs targeting human genes associated with diseases-SOD1 (ALS), JAK1 (inflammation), and HTT (HD)-to generate species-matching variants with full complementarity to their target in NHPs, mice, rats, sheep, and dogs. Variants potency and efficacy were measured in corresponding cell lines. We demonstrate that sequence, position, and number of mismatches significantly influence the ability to generate potent species-active compounds via mismatch conversion. Across tested sequences, mismatch conversion strategy ability to identify a species-active lead varied from 0% to 70%. For SOD1, lead compounds identified from species-focus screening in mouse and dog cells were more potent than leads obtained from mismatch conversion. Thus, a focused screening of therapeutic lead and model compounds may represent a more reliable strategy for the clinical advancement of siRNAs.
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Affiliation(s)
- Iris Valeria Rivera Flores
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Samuel Jackson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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3
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Ferguson CM, Sapp E, Fakih HH, Tang Q, Yamada N, Furgal RC, Paquette JD, Biscans A, Bramato BM, McHugh N, Summers A, Lochmann C, Godinho BMDC, Hildebrand S, Jackson SO, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Enhancing siRNA efficacy in vivo with extended nucleic acid backbones. Nat Biotechnol 2024:10.1038/s41587-024-02336-7. [PMID: 39090305 DOI: 10.1038/s41587-024-02336-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/25/2024] [Indexed: 08/04/2024]
Abstract
Therapeutic small interfering RNA (siRNA) requires sugar and backbone modifications to inhibit nuclease degradation. However, metabolic stabilization by phosphorothioate (PS), the only backbone chemistry used clinically, may be insufficient for targeting extrahepatic tissues. To improve oligonucleotide stabilization, we report the discovery, synthesis and characterization of extended nucleic acid (exNA) consisting of a methylene insertion between the 5'-C and 5'-OH of a nucleoside. exNA incorporation is compatible with common oligonucleotide synthetic protocols and the PS backbone, provides stabilization against 3' and 5' exonucleases and is tolerated at multiple oligonucleotide positions. A combined exNA-PS backbone enhances resistance to 3' exonuclease by ~32-fold over the conventional PS backbone and by >1,000-fold over the natural phosphodiester backbone, improving tissue exposure, tissue accumulation and efficacy in mice, both systemically and in the brain. The improved efficacy and durability imparted by exNA may enable therapeutic interventions in extrahepatic tissues, both with siRNA and with other oligonucleotides such as CRISPR guide RNA, antisense oligonucleotides, mRNA and tRNA.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Vignesh N Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Raymond C Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Joseph D Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brianna M Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Weiss A, Gilbert JW, Flores IVR, Belgrad J, Ferguson C, Dogan EO, Wightman N, Mocarski K, Echeverria D, Summers A, Bramato B, McHugh N, Furgal R, Yamada N, Cooper D, Monopoli K, Godinho BM, Hassler MR, Yamada K, Greer P, Henninger N, Brown RH, Khvorova A. RNAi-mediated silencing of SOD1 profoundly extends survival and functional outcomes in ALS mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599943. [PMID: 38979291 PMCID: PMC11230209 DOI: 10.1101/2024.06.20.599943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative condition, with 20% of familial and 2-3% of sporadic cases linked to mutations in the cytosolic superoxide dismutase (SOD1) gene. Mutant SOD1 protein is toxic to motor neurons, making SOD1 gene lowering a promising approach, supported by preclinical data and the 2023 FDA approval of the GapmeR ASO targeting SOD1, tofersen. Despite the approval of an ASO and the optimism it brings to the field, the pharmacodynamics and pharmacokinetics of therapeutic SOD1 modulation can be improved. Here, we developed a chemically stabilized divalent siRNA scaffold (di-siRNA) that effectively suppresses SOD1 expression in vitro and in vivo. With optimized chemical modification, it achieves remarkable CNS tissue permeation and SOD1 silencing in vivo. Administered intraventricularly, di-siRNASOD1 extended survival in SOD1-G93A ALS mice, surpassing survival previously seen in these mice by ASO modalities, slowed disease progression, and prevented ALS neuropathology. These properties offer an improved therapeutic strategy for SOD1-mediated ALS and may extend to other dominantly inherited neurological disorders.
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Affiliation(s)
- Alexandra Weiss
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - James W. Gilbert
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | | | - Jillian Belgrad
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Chantal Ferguson
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Elif O. Dogan
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Nicholas Wightman
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Kit Mocarski
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Ashley Summers
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Raymond Furgal
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Nozomi Yamada
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - David Cooper
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Kathryn Monopoli
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | | | - Matthew R. Hassler
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Ken Yamada
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
| | - Paul Greer
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
| | - Nils Henninger
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
- Department of Psychiatry, UMass Chan Medical School; Worcester, MA, USA
| | - Robert H. Brown
- Department of Neurology, UMass Chan Medical School; Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School; Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School; Worcester, MA, USA
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5
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Tang Q, Khvorova A. RNAi-based drug design: considerations and future directions. Nat Rev Drug Discov 2024; 23:341-364. [PMID: 38570694 PMCID: PMC11144061 DOI: 10.1038/s41573-024-00912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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6
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Liu T, Huang J, Luo D, Ren L, Ning L, Huang J, Lin H, Zhang Y. Cm-siRPred: Predicting chemically modified siRNA efficiency based on multi-view learning strategy. Int J Biol Macromol 2024; 264:130638. [PMID: 38460652 DOI: 10.1016/j.ijbiomac.2024.130638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/27/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
The rational modification of siRNA molecules is crucial for ensuring their drug-like properties. Machine learning-based prediction of chemically modified siRNA (cm-siRNA) efficiency can significantly optimize the design process of siRNA chemical modifications, saving time and cost in siRNA drug development. However, existing in-silico methods suffer from limitations such as small datasets, inadequate data representation capabilities, and lack of interpretability. Therefore, in this study, we developed the Cm-siRPred algorithm based on a multi-view learning strategy. The algorithm employs a multi-view strategy to represent the double-strand sequences, chemical modifications, and physicochemical properties of cm-siRNA. It incorporates a cross-attention model to globally correlate different representation vectors and a two-layer CNN module to learn local correlation features. The algorithm demonstrates exceptional performance in cross-validation experiments, independent dataset, and case studies on approved siRNA drugs, and showcasing its robustness and generalization ability. In addition, we developed a user-friendly webserver that enables efficient prediction of cm-siRNA efficiency and assists in the design of siRNA drug chemical modifications. In summary, Cm-siRPred is a practical tool that offers valuable technical support for siRNA chemical modification and drug efficiency research, while effectively assisting in the development of novel small nucleic acid drugs. Cm-siRPred is freely available at https://cellknowledge.com.cn/sirnapredictor/.
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Affiliation(s)
- Tianyuan Liu
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Junyang Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Delun Luo
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chengdu Jingrunze Gene Technology Company Limited, Chengdu 611138, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu 611844, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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7
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Tang Q, Gross KY, Fakih HH, Jackson SO, Zain U.I. Abideen M, Monopoli KR, Blanchard C, Bouix-Peter C, Portal T, Harris JE, Khvorova A, Alterman JF. Multispecies-targeting siRNAs for the modulation of JAK1 in the skin. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102117. [PMID: 38304729 PMCID: PMC10831156 DOI: 10.1016/j.omtn.2024.102117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Identifying therapeutic oligonucleotides that are cross-reactive to experimental animal species can dramatically accelerate the process of preclinical development and clinical translation. Here, we identify fully chemically-modified small interfering RNAs (siRNAs) that are cross-reactive to Janus kinase 1 (JAK1) in humans and a large variety of other species. We validated the identified siRNAs in silencing JAK1 in cell lines and skin tissues of multiple species. JAK1 is one of the four members of the JAK family of tyrosine kinases that mediate the signaling transduction of many inflammatory cytokine pathways. Dysregulation of these pathways is often involved in the pathogenesis of various immune disorders, and modulation of JAK family enzymes is an effective strategy in the clinic. Thus, this work may open up unprecedented opportunities for evaluating the modulation of JAK1 in many animal models of human inflammatory skin diseases. Further chemical engineering of the optimized JAK1 siRNAs may expand the utility of these compounds for treating immune disorders in additional tissues.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Katherine Y. Gross
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hassan H. Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samuel O. Jackson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Kathryn R. Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | | | - John E. Harris
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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8
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Hoogenboezem EN, Patel SS, Lo JH, Cavnar AB, Babb LM, Francini N, Gbur EF, Patil P, Colazo JM, Michell DL, Sanchez VM, McCune JT, Ma J, DeJulius CR, Lee LH, Rosch JC, Allen RM, Stokes LD, Hill JL, Vickers KC, Cook RS, Duvall CL. Structural optimization of siRNA conjugates for albumin binding achieves effective MCL1-directed cancer therapy. Nat Commun 2024; 15:1581. [PMID: 38383524 PMCID: PMC10881965 DOI: 10.1038/s41467-024-45609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
The high potential of siRNAs to silence oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, divalent lipid-conjugated siRNAs are optimized for in situ binding to albumin to improve pharmacokinetics and tumor delivery. Systematic variation of the siRNA conjugate structure reveals that the location of the linker branching site dictates tendency toward albumin association versus self-assembly, while the lipid hydrophobicity and reversibility of albumin binding also contribute to siRNA intracellular delivery. The lead structure increases tumor siRNA accumulation 12-fold in orthotopic triple negative breast cancer (TNBC) tumors over the parent siRNA. This structure achieves approximately 80% silencing of the anti-apoptotic oncogene MCL1 and yields better survival outcomes in three TNBC models than an MCL-1 small molecule inhibitor. These studies provide new structure-function insights on siRNA-lipid conjugate structures that are intravenously injected, associate in situ with serum albumin, and improve pharmacokinetics and tumor treatment efficacy.
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Affiliation(s)
- Ella N Hoogenboezem
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Shrusti S Patel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Justin H Lo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ashley B Cavnar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren M Babb
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Eva F Gbur
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Prarthana Patil
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Juan M Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Danielle L Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Violeta M Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua T McCune
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jinqi Ma
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Carlisle R DeJulius
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Linus H Lee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ryan M Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry D Stokes
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jordan L Hill
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kasey C Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Rebecca S Cook
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Craig L Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
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9
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Chernikov IV, Ponomareva UA, Meschaninova MI, Bachkova IK, Vlassov VV, Zenkova MA, Chernolovskaya EL. Cholesterol Conjugates of Small Interfering RNA: Linkers and Patterns of Modification. Molecules 2024; 29:786. [PMID: 38398538 PMCID: PMC10892548 DOI: 10.3390/molecules29040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Cholesterol siRNA conjugates attract attention because they allow the delivery of siRNA into cells without the use of transfection agents. In this study, we compared the efficacy and duration of silencing induced by cholesterol conjugates of selectively and totally modified siRNAs and their heteroduplexes of the same sequence and explored the impact of linker length between the 3' end of the sense strand of siRNA and cholesterol on the silencing activity of "light" and "heavy" modified siRNAs. All 3'-cholesterol conjugates were equally active under transfection, but the conjugate with a C3 linker was less active than those with longer linkers (C8 and C15) in a carrier-free mode. At the same time, they were significantly inferior in activity to the 5'-cholesterol conjugate. Shortening the sense strand carrying cholesterol by two nucleotides from the 3'-end did not have a significant effect on the activity of the conjugate. Replacing the antisense strand or both strands with fully modified ones had a significant effect on silencing as well as improving the duration in transfection-mediated and carrier-free modes. A significant 78% suppression of MDR1 gene expression in KB-8-5 xenograft tumors developed in mice promises an advantage from the use of fully modified siRNA cholesterol conjugates in combination chemotherapy.
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Affiliation(s)
- Ivan V Chernikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Ul'yana A Ponomareva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Mariya I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Irina K Bachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
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10
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Haraszti RA. Chimeric miRNA cluster enables multiplex and titratable gene inhibition in CAR-T cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102077. [PMID: 38059046 PMCID: PMC10696457 DOI: 10.1016/j.omtn.2023.102077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Affiliation(s)
- Reka Agnes Haraszti
- Department of Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Tuebingen, Germany
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University of Tuebingen, Tuebingen, Germany
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11
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Tang Q, Fakih HH, Zain Ui Abideen M, Hildebrand SR, Afshari K, Gross KY, Sousa J, Maebius AS, Bartholdy C, Søgaard PP, Jackerott M, Hariharan V, Summers A, Fan X, Okamura K, Monopoli KR, Cooper DA, Echeverria D, Bramato B, McHugh N, Furgal RC, Dresser K, Winter SJ, Biscans A, Chuprin J, Haddadi NS, Sherman S, Yıldız-Altay Ü, Rashighi M, Richmond JM, Bouix-Peter C, Blanchard C, Clauss A, Alterman JF, Khvorova A, Harris JE. Rational design of a JAK1-selective siRNA inhibitor for the modulation of autoimmunity in the skin. Nat Commun 2023; 14:7099. [PMID: 37925520 PMCID: PMC10625637 DOI: 10.1038/s41467-023-42714-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Inhibition of Janus kinase (JAK) family enzymes is a popular strategy for treating inflammatory and autoimmune skin diseases. In the clinic, small molecule JAK inhibitors show distinct efficacy and safety profiles, likely reflecting variable selectivity for JAK subtypes. Absolute JAK subtype selectivity has not yet been achieved. Here, we rationally design small interfering RNAs (siRNAs) that offer sequence-specific gene silencing of JAK1, narrowing the spectrum of action on JAK-dependent cytokine signaling to maintain efficacy and improve safety. Our fully chemically modified siRNA supports efficient silencing of JAK1 expression in human skin explant and modulation of JAK1-dependent inflammatory signaling. A single injection into mouse skin enables five weeks of duration of effect. In a mouse model of vitiligo, local administration of the JAK1 siRNA significantly reduces skin infiltration of autoreactive CD8+ T cells and prevents epidermal depigmentation. This work establishes a path toward siRNA treatments as a new class of therapeutic modality for inflammatory and autoimmune skin diseases.
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Affiliation(s)
- Qi Tang
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Mohammad Zain Ui Abideen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Samuel R Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Khashayar Afshari
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Katherine Y Gross
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Allison S Maebius
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | | | | | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Xueli Fan
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ken Okamura
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kathryn R Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - David A Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Raymond C Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karen Dresser
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Sarah J Winter
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jane Chuprin
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nazgol-Sadat Haddadi
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Shany Sherman
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ümmügülsüm Yıldız-Altay
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Mehdi Rashighi
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jillian M Richmond
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | | | - Adam Clauss
- LEO Pharma A/S, Industriparken 55, 2750, Ballerup, Denmark
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - John E Harris
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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12
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Lee JW, Choi J, Kim EH, Choi J, Kim SH, Yang Y. Design of siRNA Bioconjugates for Efficient Control of Cancer-Associated Membrane Receptors. ACS OMEGA 2023; 8:36435-36448. [PMID: 37810687 PMCID: PMC10552107 DOI: 10.1021/acsomega.3c05395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Research on siRNA delivery has seen tremendous growth over the past few decades. As one of the major delivery strategies, siRNA bioconjugates offer the potential to enhance and extend the pharmacological properties of siRNAs while minimizing toxicity. In this paper, we suggest the development of a siRNA conjugate platform with peptides and proteins that are ligands of target receptors for cancer treatment. The siRNA bioconjugates target and block the receptor membrane proteins, enter the cells through receptor-mediated endocytosis, and inhibit the expression of that same target membrane receptor, thereby doubly controlling the function of the membrane proteins. The three kinds of bioconjugates targeting CD47, PD-L1, and EGFR were synthesized via two different copper-free click chemistry reactions. Results showed the cellular uptake of each conjugate, reduction of target gene expression, and efficient functional control of receptor proteins. This platform provides an effective approach for regulating membrane proteins in various diseases beyond cancer.
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Affiliation(s)
- Jong Won Lee
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jiwoong Choi
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Eun Hye Kim
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department
of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jiwon Choi
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department
of Bioengineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sun Hwa Kim
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Yoosoo Yang
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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13
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Bofill-De Ros X. Toward learning the rules that predict siRNA efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:543-544. [PMID: 37588682 PMCID: PMC10425614 DOI: 10.1016/j.omtn.2023.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Affiliation(s)
- Xavier Bofill-De Ros
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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14
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Monopoli KR, Korkin D, Khvorova A. Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:93-109. [PMID: 37456778 PMCID: PMC10338369 DOI: 10.1016/j.omtn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Chemically modified small interfering RNAs (siRNAs) are promising therapeutics guiding sequence-specific silencing of disease genes. Identifying chemically modified siRNA sequences that effectively silence target genes remains challenging. Such determinations necessitate computational algorithms. Machine learning is a powerful predictive approach for tackling biological problems but typically requires datasets significantly larger than most available siRNA datasets. Here, we describe a framework applying machine learning to a small dataset (356 modified sequences) for siRNA efficacy prediction. To overcome noise and biological limitations in siRNA datasets, we apply a trichotomous, two-threshold, partitioning approach, producing several combinations of classification threshold pairs. We then test the effects of different thresholds on random forest machine learning model performance using a novel evaluation metric accounting for class imbalances. We identify thresholds yielding a model with high predictive power, outperforming a linear model generated from the same data, that was predictive upon experimental evaluation. Using a novel model feature extraction method, we observe target site base importances and base preferences consistent with our current understanding of the siRNA-mediated silencing mechanism, with the random forest providing higher resolution than the linear model. This framework applies to any classification challenge involving small biological datasets, providing an opportunity to develop high-performing design algorithms for oligonucleotide therapies.
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Affiliation(s)
- Kathryn R. Monopoli
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dmitry Korkin
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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15
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Weidner J, Kolosionek E, Holmila R, Ax E, Garreau M, Gnerlich F, Olsson H, Czechtizky W, Vollmer S, Rydzik AM. Gymnotic uptake of AntimiRs alter microRNA-34a levels in 2D and 3D epithelial cell culture. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:898-907. [PMID: 37680982 PMCID: PMC10480572 DOI: 10.1016/j.omtn.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
MicroRNAs are attractive therapeutic targets in many diseases, including chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Among microRNA inhibitors antimiRs have been proven successful in lowering aberrant microRNA levels in the clinic. We present a set of antimiRs targeting miR-34a, which has been shown to be dysregulated in chronic lung diseases. The tool compounds were taken up by a bronchial epithelial cell line and primary human bronchial epithelial cells, followed by efficient knockdown of miR-34a. Similar results were observed in 3D differentiated primary human bronchial epithelial cells cultured at the air-liquid interface. Varying chemical properties of antimiRs had significant impact on cellular uptake and potency, resulting in effective tool compounds for use in lung-relevant cellular systems. This report demonstrates gymnotic antimiR uptake and activity in 3D epithelial cell culture after apical administration, mimicking inhalation conditions.
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Affiliation(s)
- Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Reetta Holmila
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Elisabeth Ax
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Henric Olsson
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Stefan Vollmer
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Anna M. Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
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16
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O'Reilly D, Belgrad J, Ferguson C, Summers A, Sapp E, McHugh C, Mathews E, Boudi A, Buchwald J, Ly S, Moreno D, Furgal R, Luu E, Kennedy Z, Hariharan V, Monopoli K, Yang XW, Carroll J, DiFiglia M, Aronin N, Khvorova A. Di-valent siRNA-mediated silencing of MSH3 blocks somatic repeat expansion in mouse models of Huntington's disease. Mol Ther 2023; 31:1661-1674. [PMID: 37177784 PMCID: PMC10277892 DOI: 10.1016/j.ymthe.2023.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
Huntington's disease (HD) is a severe neurodegenerative disorder caused by the expansion of the CAG trinucleotide repeat tract in the huntingtin gene. Inheritance of expanded CAG repeats is needed for HD manifestation, but further somatic expansion of the repeat tract in non-dividing cells, particularly striatal neurons, hastens disease onset. Called somatic repeat expansion, this process is mediated by the mismatch repair (MMR) pathway. Among MMR components identified as modifiers of HD onset, MutS homolog 3 (MSH3) has emerged as a potentially safe and effective target for therapeutic intervention. Here, we identify a fully chemically modified short interfering RNA (siRNA) that robustly silences Msh3 in vitro and in vivo. When synthesized in a di-valent scaffold, siRNA-mediated silencing of Msh3 effectively blocked CAG-repeat expansion in the striatum of two HD mouse models without affecting tumor-associated microsatellite instability or mRNA expression of other MMR genes. Our findings establish a promising treatment approach for patients with HD and other repeat expansion diseases.
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Affiliation(s)
- Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jillian Belgrad
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cassandra McHugh
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Ella Mathews
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julianna Buchwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Moreno
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Raymond Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric Luu
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jeffery Carroll
- Behavioral Neuroscience Program, Psychology Department, Western Washington University, Bellingham, WA 98225, USA; Department of Neurology, University of Washington, Seattle, WA 98104-2499, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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17
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Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. RESEARCH SQUARE 2023:rs.3.rs-2987323. [PMID: 37398145 PMCID: PMC10312934 DOI: 10.21203/rs.3.rs-2987323/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~ 32-fold over PS backbone and > 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~ 6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
| | | | | | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Qi Tang
- University of Massachusetts Chan Medical School
| | | | | | | | | | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Bruno Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | | | - Neil Aronin
- University of Massachusetts Worcester Campus
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18
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BM, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542506. [PMID: 37292886 PMCID: PMC10245983 DOI: 10.1101/2023.05.26.542506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Vignesh Narayan Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Chantal Furguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Hassan Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Qi Tan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Raymond C. Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew R. Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
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19
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Hariharan VN, Shin M, Chang CW, O’Reilly D, Biscans A, Yamada K, Guo Z, Somasundaran M, Tang Q, Monopoli K, Krishnamurthy PM, Devi G, McHugh N, Cooper DA, Echeverria D, Cruz J, Chan IL, Liu P, Lim SY, McConnell J, Singh SP, Hildebrand S, Sousa J, Davis SM, Kennedy Z, Ferguson C, Godinho BMDC, Thillier Y, Caiazzi J, Ly S, Muhuri M, Kelly K, Humphries F, Cousineau A, Parsi KM, Li Q, Wang Y, Maehr R, Gao G, Korkin D, McDougall WM, Finberg RW, Fitzgerald KA, Wang JP, Watts JK, Khvorova A. Divalent siRNAs are bioavailable in the lung and efficiently block SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2023; 120:e2219523120. [PMID: 36893269 PMCID: PMC10089225 DOI: 10.1073/pnas.2219523120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023] Open
Abstract
The continuous evolution of SARS-CoV-2 variants complicates efforts to combat the ongoing pandemic, underscoring the need for a dynamic platform for the rapid development of pan-viral variant therapeutics. Oligonucleotide therapeutics are enhancing the treatment of numerous diseases with unprecedented potency, duration of effect, and safety. Through the systematic screening of hundreds of oligonucleotide sequences, we identified fully chemically stabilized siRNAs and ASOs that target regions of the SARS-CoV-2 genome conserved in all variants of concern, including delta and omicron. We successively evaluated candidates in cellular reporter assays, followed by viral inhibition in cell culture, with eventual testing of leads for in vivo antiviral activity in the lung. Previous attempts to deliver therapeutic oligonucleotides to the lung have met with only modest success. Here, we report the development of a platform for identifying and generating potent, chemically modified multimeric siRNAs bioavailable in the lung after local intranasal and intratracheal delivery. The optimized divalent siRNAs showed robust antiviral activity in human cells and mouse models of SARS-CoV-2 infection and represent a new paradigm for antiviral therapeutic development for current and future pandemics.
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Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ching-Wen Chang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Daniel O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zhiru Guo
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Kathryn Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - John Cruz
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Io Long Chan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Ping Liu
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sun-Young Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jill McConnell
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Satya Prakash Singh
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Sarah M. Davis
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Bruno M. D. C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yann Thillier
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Manish Muhuri
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Fiachra Humphries
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Alyssa Cousineau
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Krishna Mohan Parsi
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Qi Li
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Yang Wang
- MassBiologics, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - René Maehr
- Diabetes Center of Excellence and Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Guangping Gao
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Dmitry Korkin
- Department of Computer Science, and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA01609
| | - William M. McDougall
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Katherine A. Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA01655
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20
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Basar E, Shum B, Skaletz-Rorowski A, Wu Y, Nambiar S, Brockmeyer NH. Cholesterol-conjugated siRNAs silence gene expression in mucosal dendritic cells in cervicovaginal tissue in mice. J Eur Acad Dermatol Venereol 2023; 37:615-626. [PMID: 36331362 DOI: 10.1111/jdv.18718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND RNA interference (RNAi) provides a powerful way to investigate the role of genes in disease pathogenesis and modulate gene expression to treat disease. In 2018, the FDA approved patisiran, the first RNAi-based drug, hence paving the way for a novel class of RNAi therapeutics. Harnessing RNAi to inhibit vaginal HIV transmission requires effective gene silencing in immune cells, which remains difficult. Knockdown in accessible mucosal tissues may be easier than systemic gene silencing. Vaginally applied cholesterol-conjugated small interfering RNAs (chol-siRNAs) blocked herpes simplex virus transmission in mice without tissue damage or immunostimulation. OBJECTIVES AND METHODS To investigate using flow cytometry, confocal microscopy, and quantitative imaging if chol-siRNAs silence gene expression in vaginal immune cells in mice. RESULTS Although chol-siRNAs and lipoplexed-siRNAs silence gene expression in dendritic cells (DCs) in vitro, most internalized siRNAs concentrate within multivesicular bodies, where they are inaccessible to the cellular RNAi machinery. When applied intravaginally in vivo, chol-siRNAs penetrate the vaginal mucosa, including the lamina propria, and are efficiently internalized by intraepithelial (IE) and lamina propria (LP) DCs, and CD11b+ CD45+ cells, but not by T cells. Chol-siRNAs induce partial gene silencing in IE and LP DCs throughout the genital mucosa in vivo but are inactive in F4/80+ CD11b+ macrophages and T cells. CONCLUSION As mucosal DCs play an essential role for mucosal viral entry and dissemination, chol-siRNAs could be harnessed to target various host factors that are critical for viral uptake, DC migration and trans-infection of virions to T cells, hence allowing the development of a preventive vaginal HIV microbicide. Furthermore, chol-siRNAs could help elucidate the pathways of HIV transmission and understand the immunologic function of DCs in the genital tract.
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Affiliation(s)
- Emre Basar
- Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA.,WIR - Walk In Ruhr, Center for Sexual Health & Medicine, Department of Dermatology, Venerology and Allergology, Ruhr-Universität Bochum, Bochum, Germany.,Competence Network for HIV/AIDS, Ruhr-Universität Bochum, Bochum, Germany
| | - Bennett Shum
- Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Adriane Skaletz-Rorowski
- WIR - Walk In Ruhr, Center for Sexual Health & Medicine, Department of Dermatology, Venerology and Allergology, Ruhr-Universität Bochum, Bochum, Germany.,Competence Network for HIV/AIDS, Ruhr-Universität Bochum, Bochum, Germany
| | - Yichao Wu
- Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Sandeep Nambiar
- WIR - Walk In Ruhr, Center for Sexual Health & Medicine, Department of Dermatology, Venerology and Allergology, Ruhr-Universität Bochum, Bochum, Germany.,Competence Network for HIV/AIDS, Ruhr-Universität Bochum, Bochum, Germany
| | - Norbert H Brockmeyer
- WIR - Walk In Ruhr, Center for Sexual Health & Medicine, Department of Dermatology, Venerology and Allergology, Ruhr-Universität Bochum, Bochum, Germany.,Competence Network for HIV/AIDS, Ruhr-Universität Bochum, Bochum, Germany
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21
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Hoogenboezem EN, Patel SS, Cavnar AB, Lo JH, Babb LM, Francini N, Patil P, Colazo JM, Michell DL, Sanchez VM, McCune JT, Ma J, DeJulius CR, Lee LH, Rosch JC, Allen RM, Stokes LD, Hill JL, Vickers KC, Cook RS, Duvall CL. Structural Optimization of siRNA Conjugates for Albumin Binding Achieves Effective MCL1-Targeted Cancer Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528574. [PMID: 36824780 PMCID: PMC9948981 DOI: 10.1101/2023.02.14.528574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The high potential for therapeutic application of siRNAs to silence traditionally undruggable oncogenic drivers remains largely untapped due to the challenges of tumor cell delivery. Here, siRNAs were optimized for in situ binding to albumin through C18 lipid modifications to improve pharmacokinetics and tumor delivery. Systematic variation of siRNA conjugates revealed a lead structure with divalent C18 lipids each linked through three repeats of hexaethylene glycol connected by phosphorothioate bonds. Importantly, we discovered that locating the branch site of the divalent lipid structure proximally (adjacent to the RNA) rather than at a more distal site (after the linker segment) promotes association with albumin, while minimizing self-assembly and lipoprotein association. Comparison to higher albumin affinity (diacid) lipid variants and siRNA directly conjugated to albumin underscored the importance of conjugate hydrophobicity and reversibility of albumin binding for siRNA delivery and bioactivity in tumors. The lead conjugate increased tumor siRNA accumulation 12-fold in orthotopic mouse models of triple negative breast cancer over the parent siRNA. When applied for silencing of the anti-apoptotic oncogene MCL-1, this structure achieved approximately 80% MCL1 silencing in orthotopic breast tumors. Furthermore, application of the lead conjugate structure to target MCL1 yielded better survival outcomes in three independent, orthotopic, triple negative breast cancer models than an MCL1 small molecule inhibitor. These studies provide new structure-function insights on optimally leveraging siRNA-lipid conjugate structures that associate in situ with plasma albumin for molecular-targeted cancer therapy.
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Affiliation(s)
| | - Shrusti S. Patel
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Ashley B. Cavnar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Justin H. Lo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Lauren M. Babb
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Prarthana Patil
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Juan M. Colazo
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN
| | | | - Violeta M. Sanchez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joshua T. McCune
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Jinqi Ma
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | | | | | - Jonah C. Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN
| | - Ryan M. Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Larry D. Stokes
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Jordan L. Hill
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Rebecca S. Cook
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
| | - Craig L. Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN
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22
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Sun Y, Yu D, Geng X, Ding D, Yang Y, Liu Z, Xiao Z, Wang R, Tan W. Artificial Base-Directed In Vivo Assembly of an Albumin-siRNA Complex for Tumor-Targeting Delivery. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8872-8883. [PMID: 36751121 DOI: 10.1021/acsami.2c19075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
RNA interference (RNAi) mediated by short interfering RNA (siRNA) is a promising method for cancer treatment, but the clinical application is hampered by several limitations, including metabolic instability, lack of tumor specificity, and poor cellular uptake. To meet these challenges, we have explored the possibility of structure modification of siRNA with artificial bases for property optimization. A series of siRNAs functionalized with different numbers of hydrophobic base F are prepared for screening. The interactions of plasma proteins with F-base-modified siRNA (F-siRNA) are investigated, and it is identified that the interaction with serum albumin is dominant. Experiments revealed that the introduction of F bases conferred modified siRNA with improved tumor-specific accumulation, prolonged circulatory retention time, and better tissue permeability. Mechanistic studies indicated that the F base induces the formulation of a stable siRNA-albumin complex, which transports siRNA to tumor tissues selectively owing to an enhanced permeability and retention (EPR) effect of albumin. The F base also facilitates the binding of siRNA to transport-associated proteins on the cell membrane, enabling its cellular internalization. Together, these data demonstrate that F base modification confers siRNA-enhanced cellular uptake and biostability and specific accumulation in tumor tissue, which provides a new approach for the development of siRNA-based cancer therapeutics.
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Affiliation(s)
- Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Die Yu
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Yang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuang Liu
- Institute of Functional Nano & Soft Materials Laboratory (FUNSOM), Soochow University, Suzhou 215123, Jiangsu, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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23
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Structural Modifications of siRNA Improve Its Performance In Vivo. Int J Mol Sci 2023; 24:ijms24020956. [PMID: 36674473 PMCID: PMC9862127 DOI: 10.3390/ijms24020956] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The use of small interfering RNA (siRNA) in the clinic gives a wide range of possibilities for the treatment of previously incurable diseases. However, the main limitation for biomedical applications is their delivery to target cells and organs. Currently, delivery of siRNA to liver cells is a solved problem due to the bioconjugation of siRNA with N-acetylgalactosamine; other organs remain challenging for siRNA delivery to them. Despite the important role of the ligand in the composition of the bioconjugate, the structure and molecular weight of siRNA also play an important role in the delivery of siRNA. The basic principle is that siRNAs with smaller molecular weights are more efficient at entering cells, whereas siRNAs with larger molecular weights have advantages at the organism level. Here we review the relationships between siRNA structure and its biodistribution and activity to find new strategies for improving siRNA performance.
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24
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Lin L, Zhu S, Huang H, Wu LP, Huang J. Chemically modified small interfering RNA targeting Hedgehog signaling pathway for rheumatoid arthritis therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:88-104. [PMID: 36618268 PMCID: PMC9813581 DOI: 10.1016/j.omtn.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Rheumatoid arthritis (RA) is an inflammatory disease that leads to disability; however, existing therapies are still unsatisfactory. Activated fibroblast-like synoviocytes (FLSs) play an essential role in synovitis formation and joint destruction in RA. The Hedgehog signaling pathway is aberrantly activated and contributes to the aggressive phenotype of RA-FLSs. However, it remains uncertain whether inhibiting Smoothened (SMO), a critical component of the Hedgehog signaling pathway, is an effective treatment for RA. Here, we design a series of small interfering RNAs (siRNAs) that specifically target the SMO gene. With precise chemical modifications, siRNAs' efficacy and stability are significantly improved, and the off-target effects are minimized. The optimized chemically modified siRNA (si-S1A3-Chol) decreases RA-FLS proliferation and invasiveness without the transfection reagent. Furthermore, si-S1A3-Chol injected intra-articularly effectively alleviates joint destruction and improves motor function in collagen-induced arthritis mouse models. Consequently, our results demonstrate that chemically modified siRNA targeting the Hedgehog signaling pathway may be a potential therapy for RA.
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Affiliation(s)
- Lang Lin
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China
| | - Shangling Zhu
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China
| | - Hongyu Huang
- Division of Clinical Public Health and Institute for Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Lin-Ping Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People’s Republic of China,Corresponding author: Lin-Ping Wu, Center for Chemical Biology and Drug Discovery, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People’s Republic of China.
| | - Jianlin Huang
- Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China,Corresponding author: Jianlin Huang, Department of Rheumatology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, People’s Republic of China.
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25
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Aliyu AW, Zainuddin BS, Hou LJ, Yew LC, Mustaffa KMF. Serum Stability of 5’ Cholesterol Triethylene Glycol- 26-OKA and 3’ Cholesterol Triethylene Glycol- 24-OKA modified Protoporphyrin IX DNA-Aptamer and their in vitro Heme binding Characteristics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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26
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Conroy F, Miller R, Alterman JF, Hassler MR, Echeverria D, Godinho BMDC, Knox EG, Sapp E, Sousa J, Yamada K, Mahmood F, Boudi A, Kegel-Gleason K, DiFiglia M, Aronin N, Khvorova A, Pfister EL. Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in Huntington's disease models. Nat Commun 2022; 13:5802. [PMID: 36192390 PMCID: PMC9530163 DOI: 10.1038/s41467-022-33061-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Small interfering RNAs are a new class of drugs, exhibiting sequence-driven, potent, and sustained silencing of gene expression in vivo. We recently demonstrated that siRNA chemical architectures can be optimized to provide efficient delivery to the CNS, enabling development of CNS-targeted therapeutics. Many genetically-defined neurodegenerative disorders are dominant, favoring selective silencing of the mutant allele. In some cases, successfully targeting the mutant allele requires targeting single nucleotide polymorphism (SNP) heterozygosities. Here, we use Huntington’s disease (HD) as a model. The optimized compound exhibits selective silencing of mutant huntingtin protein in patient-derived cells and throughout the HD mouse brain, demonstrating SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. Targeting a disease-causing allele using RNAi-based therapies could be helpful in a range of dominant CNS disorders where maintaining wild-type expression is essential. Chemically modified siRNAs distinguish between mutant and normal huntingtin based on a single nucleotide difference and lower mutant huntingtin specifically in patient derived cells and in a mouse model of Huntington’s disease.
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Affiliation(s)
- Faith Conroy
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Rachael Miller
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Emily G Knox
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaquelyn Sousa
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Ken Yamada
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Farah Mahmood
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Kimberly Kegel-Gleason
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Neil Aronin
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA.,RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA.
| | - Edith L Pfister
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA.
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27
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Chemical optimization of siRNA for safe and efficient silencing of placental sFLT1. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:135-149. [PMID: 35847173 PMCID: PMC9263991 DOI: 10.1016/j.omtn.2022.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022]
Abstract
Preeclampsia (PE) is a rising, potentially lethal complication of pregnancy. PE is driven primarily by the overexpression of placental soluble fms-like tyrosine kinase 1 (sFLT1), a validated diagnostic and prognostic marker of the disease when normalized to placental growth factor (PlGF) levels. Injecting cholesterol-conjugated, fully modified, small interfering RNAs (siRNAs) targeting sFLT1 mRNA into pregnant mice or baboons reduces placental sFLT1 and ameliorates clinical signs of PE, providing a strong foundation for the development of a PE therapeutic. siRNA delivery, potency, and safety are dictated by conjugate chemistry, siRNA duplex structure, and chemical modification pattern. Here, we systematically evaluate these parameters and demonstrate that increasing 2'-O-methyl modifications and 5' chemical stabilization and using sequence-specific duplex asymmetry and a phosphocholine-docosanoic acid conjugate enhance placental accumulation, silencing efficiency and safety of sFLT1-targeting siRNAs. The optimization strategy here provides a framework for the chemical optimization of siRNAs for PE as well as other targets and clinical indications.
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28
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RNAi-based modulation of IFN-γ signaling in skin. Mol Ther 2022; 30:2709-2721. [PMID: 35477658 PMCID: PMC9372319 DOI: 10.1016/j.ymthe.2022.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 04/25/2022] [Indexed: 11/23/2022] Open
Abstract
Aberrant activation of interferon (IFN)-γ signaling plays a key role in several autoimmune skin diseases, including lupus erythematosus, alopecia areata, vitiligo, and lichen planus. Here, we identify fully chemically modified small interfering RNAs (siRNAs) that silence the ligand binding chain of the IFN-γ receptor (IFNGR1), for the modulation of IFN-γ signaling. Conjugating these siRNAs to docosanoic acid (DCA) enables productive delivery to all major skin cell types local to the injection site, with a single dose of injection supporting effective IFNGR1 protein reduction for at least 1 month in mice. In an ex vivo model of IFN-γ signaling, DCA-siRNA efficiently inhibits the induction of IFN-γ-inducible chemokines, CXCL9 and CXCL10, in skin biopsies from the injection site. Our data demonstrate that DCA-siRNAs can be engineered for functional gene silencing in skin and establish a path toward siRNA treatment of autoimmune skin diseases.
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29
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Self-delivering RNAi compounds as therapeutic agents in the central nervous system to enhance axonal regeneration after injury. iScience 2022; 25:104379. [PMID: 35620420 PMCID: PMC9127586 DOI: 10.1016/j.isci.2022.104379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 12/10/2021] [Accepted: 05/04/2022] [Indexed: 12/01/2022] Open
Abstract
The therapeutic use of RNAi has grown but often faces several hurdles related to delivery systems, compound stability, immune activation, and on-target/off-tissue effects. Self-delivering RNAi (sdRNA) molecules do not require delivery agents or excipients. Here we demonstrate the ability of sdRNA to reduce the expression of PTEN (phosphatase and tensin homolog) to stimulate regenerative axon regrowth in the injured adult CNS. PTEN-targeting sdRNA compounds were tested for efficacy in vivo by intravitreal injection after adult rat optic nerve injury. We describe critical steps in lead compound generation through the optimization of nucleotide modifications, enhancements for stability in biological matrices, and screening for off-target immunostimulatory activity. The data show that PTEN expression in vivo can be reduced using sdRNA and this enhances regeneration in adult CNS neurons after injury, raising the possibility that this method could be utilized for other clinically relevant nervous system indications. self-delivering siRNA (sdRNA) can decrease neuronal gene expression in vivo sdRNA can be successfully delivered in vivo without using vectors or excipients Phosphatase and tensin homolog (PTEN)-targeting sdRNA can enhance CNS neuronal regeneration after injury
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30
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Van Hoeck J, Braeckmans K, De Smedt SC, Raemdonck K. Non-viral siRNA delivery to T cells: Challenges and opportunities in cancer immunotherapy. Biomaterials 2022; 286:121510. [DOI: 10.1016/j.biomaterials.2022.121510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 03/17/2022] [Accepted: 04/01/2022] [Indexed: 12/12/2022]
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31
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Yang C, Zhao H, Sun Y, Wang C, Geng X, Wang R, Tang L, Han D, Liu J, Tan W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3083-3095. [PMID: 35293579 PMCID: PMC8989545 DOI: 10.1093/nar/gkac156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Cheng Wang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ruowen Wang
- To whom correspondence should be addressed. Tel: +86 02168385698; Fax:+86 02168385698;
| | - Lumin Tang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianjun Liu
- Correspondence may also be addressed to Jianjun Liu.
| | - Weihong Tan
- Correspondence may also be addressed to Weihong Tan.
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32
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Barkau CL, O'Reilly D, Eddington SB, Damha MJ, Gagnon KT. Small nucleic acids and the path to the clinic for anti-CRISPR. Biochem Pharmacol 2021; 189:114492. [PMID: 33647260 PMCID: PMC8725204 DOI: 10.1016/j.bcp.2021.114492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.
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Affiliation(s)
- Christopher L Barkau
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Seth B Eddington
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
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33
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Aghamiri S, Raee P, Talaei S, Mohammadi-Yeganeh S, Bayat S, Rezaee D, Ghavidel AA, Teymouri A, Roshanzamiri S, Farhadi S, Ghanbarian H. Nonviral siRNA delivery systems for pancreatic cancer therapy. Biotechnol Bioeng 2021; 118:3669-3690. [PMID: 34170520 DOI: 10.1002/bit.27869] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 12/17/2022]
Abstract
The serious drawbacks of the conventional treatment of pancreatic ductal adenocarcinoma (PDAC) such as nonspecific toxicity and high resistance to chemo and radiation therapy, have prompted the development and application of countless small interfering RNA (siRNA)-based therapeutics. Recent advances in drug delivery systems hold great promise for improving siRNA-based therapeutics and developing a new class of drugs, known as nano-siRNA drugs. However, many fundamental questions, regarding toxicity, immunostimulation, and poor knowledge of nano-bio interactions, need to be addressed before clinical translation. In this review, we provide recent achievements in the design and development of various nonviral delivery vehicles for pancreatic cancer therapy. More importantly, codelivery of conventional anticancer drugs with siRNA as a new revolutionary pancreatic cancer combinational therapy is completely discussed.
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Affiliation(s)
- Shahin Aghamiri
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pourya Raee
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sam Talaei
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shiva Bayat
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Delsuz Rezaee
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin A Ghavidel
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Teymouri
- Department of Infectious Disease, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheil Roshanzamiri
- Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shohreh Farhadi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Tissue Engineering and Applied Cell SciencesSchool of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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34
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Subhan MA, Attia SA, Torchilin VP. Advances in siRNA delivery strategies for the treatment of MDR cancer. Life Sci 2021; 274:119337. [PMID: 33713664 DOI: 10.1016/j.lfs.2021.119337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022]
Abstract
RNA interference (RNAi) represents a promising therapeutic method that uses siRNA for cancer treatment. Although the RNAi technique has been increasingly used for clinical trials, systemic siRNA delivery into targeted cells is still challenging. The barriers impeding siRNA therapeutics delivery and impacting the treatment outcome must overcome with negligible systemic toxicity for a desirable and successful delivery of siRNA to MDR cancer cells. Nano delivery strategies have been investigated for nanocarrier functionalization, cancer immunotherapy and cancer targeting. Lipid nanoparticles (LNPs), dynamic polyconjugates (DPC™), GalNAc-siRNA conjugates, exosome and RBC systems have shown potential for efficient delivery of siRNA to cancer cells. Delivery of siRNA to tumor cells, immune cells to regulate T cell functions for immunotherapy are promising approaches.
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Affiliation(s)
- Md Abdus Subhan
- Department of Chemistry, ShahJalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Sara Aly Attia
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Vladimir P Torchilin
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA; Department of Oncology, Radiotherapy and Plastic Surgery I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.
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35
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Portet A, Galinier R, Lassalle D, Faille A, Gourbal B, Duval D. Hemocyte siRNA uptake is increased by 5' cholesterol-TEG addition in Biomphalaria glabrata, snail vector of schistosome. PeerJ 2021; 9:e10895. [PMID: 33665030 PMCID: PMC7908872 DOI: 10.7717/peerj.10895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022] Open
Abstract
Biomphalaria glabrata is one of the snail intermediate hosts of Schistosoma mansoni, the causative agent of intestinal schistosomiasis disease. Numerous molecular studies using comparative approaches between susceptible and resistant snails to S. mansoni infection have helped identify numerous snail key candidates supporting such susceptible/resistant status. The functional approach using RNA interference (RNAi) remains crucial to validate the function of such candidates. CRISPR-Cas systems are still under development in many laboratories, and RNA interference remains the best tool to study B. glabrata snail genetics. Herein, we describe the use of modified small interfering RNA (siRNA) molecules to enhance cell delivery, especially into hemocytes, the snail immune cells. Modification of siRNA with 5′ Cholesteryl TriEthylene Glycol (Chol-TEG) promotes cellular uptake by hemocytes, nearly eightfold over that of unmodified siRNA. FACS analysis reveals that more than 50% of hemocytes have internalized Chol-TEG siRNA conjugated to Cy3 fluorophores, 2 hours only after in vivo injection into snails. Chol-TEG siRNA targeting BgTEP1 (ThioEster-containing Protein), a parasite binding protein, reduced BgTEP1 transcript expression by 70–80% compared to control. The level of BgTEP1 protein secreted in the hemolymph was also decreased. However, despite the BgTEP1 knock-down at both RNA and protein levels, snail compatibility with its sympatric parasite is not affected suggesting functional redundancy among the BgTEP genes family in snail-schistosoma interaction.
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Affiliation(s)
- Anaïs Portet
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France.,Department of Medicine, Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - Richard Galinier
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Damien Lassalle
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Alexandre Faille
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Benjamin Gourbal
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - David Duval
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
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36
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Golubeva TS, Cherenko VA, Orishchenko KE. Recent Advances in the Development of Exogenous dsRNA for the Induction of RNA Interference in Cancer Therapy. Molecules 2021; 26:701. [PMID: 33572762 PMCID: PMC7865971 DOI: 10.3390/molecules26030701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 11/17/2022] Open
Abstract
Selective regulation of gene expression by means of RNA interference has revolutionized molecular biology. This approach is not only used in fundamental studies on the roles of particular genes in the functioning of various organisms, but also possesses practical applications. A variety of methods are being developed based on gene silencing using dsRNA-for protecting agricultural plants from various pathogens, controlling insect reproduction, and therapeutic techniques related to the oncological disease treatment. One of the main problems in this research area is the successful delivery of exogenous dsRNA into cells, as this can be greatly affected by the localization or origin of tumor. This overview is dedicated to describing the latest advances in the development of various transport agents for the delivery of dsRNA fragments for gene silencing, with an emphasis on cancer treatment.
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Affiliation(s)
- Tatiana S. Golubeva
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk 630090, Russia; (V.A.C.); (K.E.O.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Viktoria A. Cherenko
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk 630090, Russia; (V.A.C.); (K.E.O.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Konstantin E. Orishchenko
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk 630090, Russia; (V.A.C.); (K.E.O.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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37
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Boumil EF, Castro N, Phillips AT, Chatterton JE, McCauley SM, Wolfson AD, Shmushkovich T, Ridilla M, Bernstein AM. USP10 Targeted Self-Deliverable siRNA to Prevent Scarring in the Cornea. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:1029-1043. [PMID: 32829179 PMCID: PMC7452140 DOI: 10.1016/j.omtn.2020.07.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/17/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023]
Abstract
Ocular scarring after surgery, trauma, or infection leads to vision loss. The transparent cornea is an excellent model system to test anti-scarring therapies. Cholesterol-conjugated fully modified asymmetric small interfering RNAs (siRNAs) (self-deliverable siRNAs [sdRNAs]) are a novel modality for in vivo gene knockdown, transfecting cells and tissues without any additional formulations. Myofibroblasts are a main contributor to scarring and fibrosis. αv integrins play a central role in myofibroblast pathological adhesion, overcontraction, and transforming growth factor β (TGF-β) activation. Previously, we demonstrated that αv integrins are protected from intracellular degradation after wounding by upregulation of the deubiquitinase (DUB) ubiquitin-specific protease 10 (USP10), leading to integrin cell surface accumulation. In this study, we tested whether knockdown of USP10 with a USP10-targeting sdRNA (termed US09) will reduce scarring after wounding a rabbit cornea in vivo. The wounded corneal stroma was treated once with US09 or non-targeting control (NTC) sdRNA. At 6 weeks US09 treatment resulted in faster wound closure, limited scarring, and suppression of fibrotic markers and immune response. Specifically, fibronectin-extra domain A (EDA), collagen III, and a-smooth muscle actin (p < 0.05), CD45+ cell infiltration (p < 0.01), and apoptosis at 24 (p < 0.01) and 48 h (p < 0.05) were reduced post-wounding. Corneal thickness and cell proliferation were restored to unwounded parameters. Targeting the DUB, USP10 is a novel strategy to reduce scarring. This study indicates that ubiquitin-mediated pathways should be considered in the pathogenesis of fibrotic healing.
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Affiliation(s)
- Edward F Boumil
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Nileyma Castro
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Andrew T Phillips
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | | | | | | | | | - Marc Ridilla
- Repair Biotechnologies, 841 East Fayette Street, Syracuse, NY 13210, USA
| | - Audrey M Bernstein
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.
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38
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Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
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Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
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39
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Basiri B, Xie F, Wu B, Humphreys SC, Lade JM, Thayer MB, Yamaguchi P, Florio M, Rock BM. Introducing an In Vitro Liver Stability Assay Capable of Predicting the In Vivo Pharmacodynamic Efficacy of siRNAs for IVIVC. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:725-736. [PMID: 32771924 PMCID: PMC7415771 DOI: 10.1016/j.omtn.2020.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/18/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023]
Abstract
There has been a renewed interest in therapeutic small interfering RNAs (siRNAs) over the past few years. This is particularly the result of successful and efficient delivery of N-acetylgalactosamine (GalNAc)-conjugated siRNAs to the liver. In general, the lead selection process for siRNA drugs is faster and more straightforward than traditional small molecules. Nevertheless, many siRNAs of different sequences and chemical modification patterns must still be evaluated before arriving at a final candidate. One of the major difficulties in streamlining this workflow is the well-known phenomenon that the in vitro data obtained from oligonucleotides transfected into cells are not directly predictive of their in vivo activity. Consequently, all oligonucleotides with some degree of in vitro activity are typically screened in vivo before final lead selection. Here, we demonstrate that the stability of liver-targeting GalNAc-conjugated siRNAs in a mouse liver homogenate shows an acceptable correlation to their in vivo target knockdown efficacy. Therefore, we suggest the incorporation of an in vitro liver homogenate stability assay during the lead optimization process for siRNAs. The addition of this assay to a flow scheme may decrease the need for animal studies, and it could bring cost savings and increase efficiency in siRNA drug development.
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Affiliation(s)
- Babak Basiri
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA.
| | - Fang Xie
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA
| | - Bin Wu
- Amgen Research, Hybrid Modality Engineering, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Sara C Humphreys
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA
| | - Julie M Lade
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA
| | - Mai B Thayer
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA
| | - Pam Yamaguchi
- Amgen Research, Cardiometabolic Disorders, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Monica Florio
- Amgen Research, Cardiometabolic Disorders, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Brooke M Rock
- Amgen Research, Pharmacokinetics and Drug Metabolism, 1120 Veterans Blvd., South San Francisco, CA 94080, USA
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40
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Davis SM, Sousa J, Vangjeli L, Hassler MR, Echeverria D, Knox E, Turanov AA, Alterman JF, Khvorova A. 2'-O-Methyl at 20-mer Guide Strand 3' Termini May Negatively Affect Target Silencing Activity of Fully Chemically Modified siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:266-277. [PMID: 32610253 PMCID: PMC7327867 DOI: 10.1016/j.omtn.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Small interfering RNAs (siRNAs) have the potential to treat a broad range of diseases. siRNAs need to be extensively chemically modified to improve their bioavailability, safety, and stability in vivo. However, chemical modifications variably impact target silencing for different siRNA sequences, making the activity of chemically modified siRNA difficult to predict. Here, we systematically evaluated the impact of 3′ terminal modifications (2′-O-methyl versus 2′-fluoro) on guide strands of different length and showed that 3′ terminal 2′-O-methyl modification negatively impacts activity for >60% of siRNA sequences tested but only in the context of 20- and not 19- or 21-nt-long guide strands. These results indicate that sequence, modification pattern, and structure may cooperatively affect target silencing. Interestingly, the introduction of an extra 2′-fluoro modification in the seed region at guide strand position 5, but not 7, may partially compensate for the negative impact of 3′ terminal 2′-O-methyl modification. Molecular modeling analysis suggests that 2′-O-methyl modification may impair guide strand interactions within the PAZ domain of argonaute-2, which may affect target recognition and cleavage, specifically when guide strands are 20-nt long. Our findings emphasize the complex nature of modified RNA-protein interactions and contribute to design principles for chemically modified siRNAs.
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Affiliation(s)
- Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lorenc Vangjeli
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Emily Knox
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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41
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Segal M, Biscans A, Gilles ME, Anastasiadou E, De Luca R, Lim J, Khvorova A, Slack FJ. Hydrophobically Modified let-7b miRNA Enhances Biodistribution to NSCLC and Downregulates HMGA2 In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:267-277. [PMID: 31855835 PMCID: PMC6926262 DOI: 10.1016/j.omtn.2019.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have increasingly been shown to be involved in human cancer, and interest has grown about the potential use of miRNAs for cancer therapy. miRNA levels are known to be altered in cancer cells, including in non-small cell lung cancer (NSCLC), a subtype of lung cancer that is the most prevalent form of cancer worldwide and that lacks effective therapies. The let-7 miRNA is involved in the regulation of oncogene expression in cells and directly represses cancer growth in the lung. let-7 is therefore a potential molecular target for tumor therapy. However, applications of RNA interference for cancer research have been limited by a lack of simple and efficient methods to deliver oligonucleotides (ONs) to cancer cells. In this study, we have used in vitro and in vivo approaches to show that HCC827 cells internalize hydrophobically modified let-7b miRNAs (hmiRNAs) added directly to the culture medium without the need for lipid formulation. We identified functional let-7b hmiRNAs targeting the HMGA2 mRNA, one of the let-7 target genes upregulated in NSCLC, and show that direct uptake in HCC827 cells induced potent and specific gene silencing in vitro and in vivo. Thus, hmiRNAs constitute a novel class of ONs that enable functional studies of genes involved in cancer biology and are potentially therapeutic molecules.
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Affiliation(s)
- Meirav Segal
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maud-Emmanuelle Gilles
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Eleni Anastasiadou
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Roberto De Luca
- HMS Initiative for RNA Medicine, Department of Neurology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Jihoon Lim
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA.
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42
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Sioud M. Unleashing the Therapeutic Potential of Dendritic and T Cell Therapies Using RNA Interference. Methods Mol Biol 2020; 2115:259-280. [PMID: 32006406 DOI: 10.1007/978-1-0716-0290-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Therapeutic dendritic cell (DC) cancer vaccines work to boost the body's immune system to fight a cancer. Although this type of immunotherapy often leads to the activation of tumor-specfic T cells, clinical responses are fairly low, arguing for the need to improve the design of DC-based vaccines. Recent studies revealed a promising strategy of combining DC vaccines with small interfering RNAs (siRNAs) targeting immunosuppressive signals such as checkpoint receptors. Similarly, incorporating checkpoint siRNA blockers in adoptive T-cell therapy to amplify cytotoxic T lymphocyte responses is now being tested in the clinic. The development of the next generation of cancer immunotherapies using siRNA technology will hopefuly benefit patients with various cancer types including those who did not respond to current therapies. This review highlights the latest advances in RNA interference technology to improve the therapeutic efficacy of DC cancer vaccines and T cell therapy.
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Affiliation(s)
- Mouldy Sioud
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Ullernchausseen 70, Oslo, Norway.
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43
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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44
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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45
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Chevalier R. siRNA Targeting and Treatment of Gastrointestinal Diseases. Clin Transl Sci 2019; 12:573-585. [PMID: 31309709 PMCID: PMC6853152 DOI: 10.1111/cts.12668] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
Abstract
RNA interference via small interfering RNA (siRNA) offers opportunities to precisely target genes that contribute to gastrointestinal (GI) pathologies, such as inflammatory bowel disease, celiac, and esophageal scarring. Delivering the siRNA to the GI tract proves challenging as the harsh environment of the intestines degrades the siRNA before it can reach its target or blocks its entry into its site of action in the cytoplasm. Additionally, the GI tract is large and disease is often localized to a specific site. This review discusses polymer and lipid‐based delivery systems for protection and targeting of siRNA therapies to the GI tract to treat local disease.
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Affiliation(s)
- Rachel Chevalier
- Children's Mercy Kansas City, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
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46
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Current Aspects of siRNA Bioconjugate for In Vitro and In Vivo Delivery. Molecules 2019; 24:molecules24122211. [PMID: 31200490 PMCID: PMC6631009 DOI: 10.3390/molecules24122211] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on siRNA delivery have seen intense growth in the past decades since siRNA has emerged as a new class of gene therapeutics for the treatment of various diseases. siRNA bioconjugate, as one of the major delivery strategies, offers the potential to enhance and broaden pharmacological properties of siRNA, while minimizing the heterogeneity and stability-correlated toxicology. This review summarizes the recent developments of siRNA bioconjugate, including the conjugation with antibody, peptide, aptamer, small chemical, lipidoid, cell-penetrating peptide polymer, and nanoparticle. These siRNA bioconjugate, either administrated alone or formulated with other agents, could significantly improve pharmacokinetic behavior, enhance the biological half-life, and increase the targetability while maintaining sufficient gene silencing activity, with a concomitant improvement of the therapeutic outcomes and diminishment of adverse effects. This review emphasizes the delivery application of these siRNA bioconjugates, especially the conjugation strategy that control the integrity, stability and release of siRNA bioconjugates. The limitations conferred by these conjugation strategies have also been covered.
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47
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Weng Y, Xiao H, Zhang J, Liang XJ, Huang Y. RNAi therapeutic and its innovative biotechnological evolution. Biotechnol Adv 2019; 37:801-825. [PMID: 31034960 DOI: 10.1016/j.biotechadv.2019.04.012] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 04/09/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
Abstract
Recently, United States Food and Drug Administration (FDA) and European Commission (EC) approved Alnylam Pharmaceuticals' RNA interference (RNAi) therapeutic, ONPATTRO™ (Patisiran), for the treatment of the polyneuropathy of hereditary transthyretin-mediated (hATTR) amyloidosis in adults. This is the first RNAi therapeutic all over the world, as well as the first FDA-approved treatment for this indication. As a milestone event in RNAi pharmaceutical industry, it means, for the first time, people have broken through all development processes for RNAi drugs from research to clinic. With this achievement, RNAi approval may soar in the coming years. In this paper, we introduce the basic information of ONPATTRO and the properties of RNAi and nucleic acid therapeutics, update the clinical and preclinical development activities, review its complicated development history, summarize the key technologies of RNAi at early stage, and discuss the latest advances in delivery and modification technologies. It provides a comprehensive view and biotechnological insights of RNAi therapy for the broader audiences.
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Affiliation(s)
- Yuhua Weng
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, PR China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jinchao Zhang
- College of Chemistry & Environmental Science, Chemical Biology Key Laboratory of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Hebei University, Baoding 071002, PR China
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS) Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, PR China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, PR China.
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48
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Whitehouse WL, Noble JE, Ryadnov MG, Howorka S. Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures. Bioconjug Chem 2019; 30:1836-1844. [PMID: 30821443 DOI: 10.1021/acs.bioconjchem.9b00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanostructures constitute a rapidly advancing tool-set for exploring cell-membrane functions and intracellular sensing or advancing delivery of biomolecular cargo into cells. Chemical conjugation with lipid anchors can mediate binding of DNA nanostructures to synthetic lipid bilayers, yet how such structures interact with biological membranes and internalize cells has not been shown. Here, an archetypal 6-duplex nanobundle is used to investigate how lipid conjugation influences DNA cell binding and internalization kinetics. Cellular interactions of DNA nanobundles modified with one and three cholesterol anchors were assessed using flow cytometry and confocal microscopy. Nuclease digestion was used to distinguish surface-bound DNA, which is nuclease accessible, from internalized DNA. Three cholesterol anchors were found to enhance cellular association by up to 10-fold when compared with unmodified DNA. The bundles were endocytosed efficiently within 24 h. The results can help design controlled DNA binding and trafficking into cells.
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Affiliation(s)
- William L Whitehouse
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - James E Noble
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Stefan Howorka
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
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49
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Sioud M. Releasing the Immune System Brakes Using siRNAs Enhances Cancer Immunotherapy. Cancers (Basel) 2019; 11:cancers11020176. [PMID: 30717461 PMCID: PMC6406640 DOI: 10.3390/cancers11020176] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/12/2022] Open
Abstract
Therapeutic dendritic cell (DC) cancer vaccines rely on the immune system to eradicate tumour cells. Although tumour antigen-specific T cell responses have been observed in most studies, clinical responses are fairly low, arguing for the need to improve the design of DC-based vaccines. The incorporation of small interfering RNAs (siRNAs) against immunosuppressive factors in the manufacturing process of DCs can turn the vaccine into potent immune stimulators. Additionally, siRNA modification of ex vivo-expanded T cells for adoptive immunotherapy enhanced their killing potency. Most of the siRNA-targeted immune inhibitory factors have been successful in that their blockade produced the strongest cytotoxic T cell responses in preclinical and clinical studies. Cancer patients treated with the siRNA-modified DC vaccines showed promising clinical benefits providing a strong rationale for further development of these immunogenic vaccine formulations. This review covers the progress in combining siRNAs with DC vaccines or T cell therapy to boost anti-tumour immunity.
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Affiliation(s)
- Mouldy Sioud
- Department of Immunology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Montebello, N-0310 Oslo, Norway.
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