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Bishani A, Meschaninova MI, Zenkova MA, Chernolovskaya EL. The Impact of Chemical Modifications on the Interferon-Inducing and Antiproliferative Activity of Short Double-Stranded Immunostimulating RNA. Molecules 2024; 29:3225. [PMID: 38999177 PMCID: PMC11243415 DOI: 10.3390/molecules29133225] [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: 05/30/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
A short 19 bp dsRNA with 3'-trinucleotide overhangs acting as immunostimulating RNA (isRNA) demonstrated strong antiproliferative action against cancer cells, immunostimulatory activity through activation of cytokines and Type-I IFN secretion, as well as anti-tumor and anti-metastatic effects in vivo. The aim of this study was to determine the tolerance of chemical modifications (2'-F, 2'-OMe, PS, cholesterol, and amino acids) located at different positions within this isRNA to its ability to activate the innate immune system. The obtained duplexes were tested in vivo for their ability to activate the synthesis of interferon-α in mice, and in tumor cell cultures for their ability to inhibit their proliferation. The obtained data show that chemical modifications in the composition of isRNA have different effects on its individual functions, including interferon-inducing and antiproliferative effects. The effect of modifications depends not only on the type of modification but also on its location and the surrounding context of the modifications. This study made it possible to identify leader patterns of modifications that enhance the properties of isRNA: F2/F2 and F2_S/F2 for interferon-inducing activity, as well as F2_S5/F2_S5, F2-NH2/F2-NH2, and Ch-F2/Ch-F2 for antiproliferative action. These modifications can improve the pharmacokinetic and pharmacodynamic properties, as well as increase the specificity of isRNA action to obtain the desired effect.
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Affiliation(s)
| | | | | | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.B.); (M.I.M.); (M.A.Z.)
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2
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Belgrad J, Tang Q, Hildebrand S, Summers A, Sapp E, Echeverria D, O’Reilly D, Luu E, Bramato B, Allen S, Cooper D, Alterman J, Yamada K, Aronin N, DiFiglia M, Khvorova A. A programmable dual-targeting siRNA scaffold supports potent two-gene modulation in the central nervous system. Nucleic Acids Res 2024; 52:6099-6113. [PMID: 38726879 PMCID: PMC11194107 DOI: 10.1093/nar/gkae368] [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] [Received: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
Divalent short-interfering RNA (siRNA) holds promise as a therapeutic approach allowing for the sequence-specific modulation of a target gene within the central nervous system (CNS). However, an siRNA modality capable of simultaneously modulating gene pairs would be invaluable for treating complex neurodegenerative disorders, where more than one pathway contributes to pathogenesis. Currently, the parameters and scaffold considerations for multi-targeting nucleic acid modalities in the CNS are undefined. Here, we propose a framework for designing unimolecular 'dual-targeting' divalent siRNAs capable of co-silencing two genes in the CNS. We systematically adjusted the original CNS-active divalent siRNA and identified that connecting two sense strands 3' and 5' through an intra-strand linker enabled a functional dual-targeting scaffold, greatly simplifying the synthetic process. Our findings demonstrate that the dual-targeting siRNA supports at least two months of maximal distribution and target silencing in the mouse CNS. The dual-targeting divalent siRNA is highly programmable, enabling simultaneous modulation of two different disease-relevant gene pairs (e.g. Huntington's disease: MSH3 and HTT; Alzheimer's disease: APOE and JAK1) with similar potency to a mixture of single-targeting divalent siRNAs against each gene. This work enhances the potential for CNS modulation of disease-related gene pairs using a unimolecular siRNA.
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Affiliation(s)
- Jillian Belgrad
- 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
| | - Sam Hildebrand
- 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
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital; Charlestown, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Dan O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Eric Luu
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Sarah Allen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Julia Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, MA, USA
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, 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
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital; Charlestown, 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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3
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Hariharan VN, Nakamura T, Shin M, Tang Q, Sontakke V, Caiazzi J, Hildebrand S, Khvorova A, Yamada K. Phosphatidylcholine head group chemistry alters the extrahepatic accumulation of lipid-conjugated siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102230. [PMID: 38938759 PMCID: PMC11209015 DOI: 10.1016/j.omtn.2024.102230] [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: 02/07/2024] [Accepted: 05/22/2024] [Indexed: 06/29/2024]
Abstract
Small interfering RNAs (siRNAs) are revolutionizing the treatment of liver-associated indications. Yet, robust delivery to extrahepatic tissues remains a challenge. Conjugating lipids (e.g., docosanoic acid [DCA]) to siRNA supports extrahepatic delivery, but tissue accumulation remains lower than that achieved in liver by approved siRNA therapeutics. Early evidence suggests that functionalizing DCA with a head group (e.g., phosphatidylcholine [PC]) may enhance delivery to certain tissues. Here, we report the first systematic evaluation of the effect of PC head group chemistry on the extrahepatic distribution of DCA-conjugated siRNAs. We show that functionalizing DCA with a PC head group enhances siRNA accumulation in heart, muscle, lung, pancreas, duodenum, urinary bladder, and fat. Varying the size of the linker between the phosphate and choline moiety of the PC head group altered the extrahepatic accumulation of siRNA, with the optimal linker length being different for different tissues. Increasing PC head group valency also improved extrahepatic accumulation in a tissue-specific manner. This study demonstrates the structural impact of the PC moiety on the biodistribution of lipid-conjugated siRNA and introduces multiple novel PC variants for the chemical optimization of DCA-conjugated siRNA. These chemical variants can be used in the context of other lipids to increase the repertoire of conjugates for the extrahepatic distribution of siRNAs.
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Affiliation(s)
- Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Takahiro Nakamura
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Vyankat Sontakke
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samuel Hildebrand
- 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
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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4
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Sorets AG, Schwensen KR, Francini N, Kjar A, Abdulrahman AM, Shostak A, Katdare KA, Schoch KM, Cowell RP, Park JC, Ligocki AP, Ford WT, Ventura-Antunes L, Hoogenboezem EN, Prusky A, Castleberry M, Michell DL, Miller TM, Vickers KC, Schrag MS, Duvall CL, Lippmann ES. Lipid-siRNA conjugate accesses a perivascular transport mechanism and achieves widespread and durable knockdown in the central nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598079. [PMID: 38915549 PMCID: PMC11195074 DOI: 10.1101/2024.06.09.598079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Short-interfering RNA (siRNA) has gained significant interest for treatment of neurological diseases by providing the capacity to achieve sustained inhibition of nearly any gene target. Yet, achieving efficacious drug delivery throughout deep brain structures of the CNS remains a considerable hurdle. We herein describe a lipid-siRNA conjugate that, following delivery into the cerebrospinal fluid (CSF), is transported effectively through perivascular spaces, enabling broad dispersion within CSF compartments and through the CNS parenchyma. We provide a detailed examination of the temporal kinetics of gene silencing, highlighting potent knockdown for up to five months from a single injection without detectable toxicity. Single-cell RNA sequencing further demonstrates gene silencing activity across diverse cell populations in the parenchyma and at brain borders, which may provide new avenues for neurological disease-modifying therapies.
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Affiliation(s)
- Alexander G. Sorets
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Katrina R. Schwensen
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nora Francini
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Andrew Kjar
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Adam M. Abdulrahman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alena Shostak
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ketaki A. Katdare
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Kathleen M. Schoch
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Rebecca P. Cowell
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Joshua C. Park
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alexander P. Ligocki
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - William T. Ford
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | | | - Alex Prusky
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark Castleberry
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Danielle L. Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy M. Miller
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew S. Schrag
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Craig L. Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ethan S. Lippmann
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
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5
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Gonzalez-Candia A, Figueroa EG, Krause BJ. Pharmacological and molecular mechanisms of miRNA-based therapies for targeting cardiovascular dysfunction. Biochem Pharmacol 2024:116318. [PMID: 38801924 DOI: 10.1016/j.bcp.2024.116318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Advances in understanding gene expression regulation through epigenetic mechanisms have contributed to elucidating the regulatory mechanisms of noncoding RNAs as pharmacological targets in several diseases. MicroRNAs (miRs) are a class of evolutionarily conserved, short, noncoding RNAs regulating in a concerted manner gene expression at the post-transcriptional level by targeting specific sequences of the 3'-untranslated region of mRNA. Conversely, mechanisms of cardiovascular disease (CVD) remain largely elusive due to their life-course origins, multifactorial pathophysiology, and co-morbidities. In this regard, CVD treatment with conventional medications results in therapeutic failure due to progressive resistance to monotherapy, which overlooks the multiple factors involved, and reduced adherence to poly-pharmacology approaches. Consequently, considering its role in regulating complete gene pathways, miR-based drugs have appreciably progressed into preclinical and clinical testing. This review summarizes the current knowledge about the mechanisms of miRs in cardiovascular disease, focusing specifically on describing how clinical chemistry and physics have improved the stability of the miR molecule. In addition, a comprehensive review of the main miRs involved in cardiovascular disease and the clinical trials in which these molecules are used as active pharmacological molecules is provided.
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Affiliation(s)
- Alejandro Gonzalez-Candia
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Esteban G Figueroa
- Laboratory of Fetal Neuroprogramming (www.neurofetal-lab.cl), Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile
| | - Bernardo J Krause
- Institute of Health Sciences, Universidad de O'Higgins, Rancagua, Chile.
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6
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Kremer A, Ryaykenen T, Haraszti RA. Systematic optimization of siRNA productive uptake into resting and activated T cells ex vivo. Biomed Pharmacother 2024; 172:116285. [PMID: 38382331 DOI: 10.1016/j.biopha.2024.116285] [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: 11/24/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024] Open
Abstract
RNA-based medicines are ideally suited for precise modulation of T cell phenotypes in anti-cancer immunity, in autoimmune diseases and for ex vivo modulation of T-cell-based therapies. Therefore, understanding productive siRNA uptake to T cells is of particular importance. Most studies used unmodified siRNAs or commercially available siRNAs with undisclosed chemical modification patterns to show functionality in T cells. Despite being an active field of research, robust siRNA delivery to T cells still represents a formidable challenge. Therefore, a systematic approach is needed to further optimize and understand productive siRNA uptake pathways to T cells. Here, we compared conjugate-mediated and nanoparticle-mediated delivery of siRNAs to T cells in the context of fully chemically modified RNA constructs. We showed that lipid-conjugate-mediated delivery outperforms lipid-nanoparticle-mediated and extracellular-vesicle-mediated delivery in activated T cells ex vivo. Yet, ex vivo manipulation of T cells without the need of activation is of great therapeutic interest for CAR-T, engineered TCR-T and allogeneic donor lymphocyte applications. We are first to report productive siRNA uptake into resting T cells using lipid-conjugate-mediated delivery. Interestingly, we observed strong dependence of silencing activity on lipid-conjugate-identity in resting T cells but not in activated T cells. This phenomenon is consistent with our early uptake kinetics data. Lipid-conjugates also enabled delivery of siRNA to all mononuclear immune cell types, including both lymphoid and myeloid lineages. These findings are expected to be broadly applicable for ex vivo modulation of immune cell therapies.
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Affiliation(s)
- A Kremer
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany
| | - T Ryaykenen
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany
| | - R A Haraszti
- Department of Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Germany; Gene and RNA Therapy Center (GRTC), Faculty of Medicine, University Tuebingen, Germany.
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7
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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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8
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Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Amrani N, Chen Z, Gaston N, Wagh A, Newby G, Xie J, Liu DR, Gao G, Wolfe S, Khvorova A, Watts J, Sontheimer E. Self-delivering, chemically modified CRISPR RNAs for AAV co-delivery and genome editing in vivo. Nucleic Acids Res 2024; 52:977-997. [PMID: 38033325 PMCID: PMC10810193 DOI: 10.1093/nar/gkad1125] [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] [Received: 03/09/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a 'protecting oligo'), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
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Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, 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
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Atish Wagh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Scot A Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Molecular, Cell and Cancer Biology, 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
- NeuroNexus 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
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Erik J Sontheimer
- 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
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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9
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Hofman CR, Corey DR. Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges. Cell Chem Biol 2024; 31:125-138. [PMID: 37804835 PMCID: PMC10841528 DOI: 10.1016/j.chembiol.2023.09.005] [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] [Received: 07/05/2023] [Revised: 08/27/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023]
Abstract
Synthetic antisense oligonucleotides (ASOs) and duplex RNAs (dsRNAs) are an increasingly successful strategy for drug development. After a slow start, the pace of success has accelerated since the approval of Spinraza (nusinersen) in 2016 with several drug approvals. These accomplishments have been achieved even though oligonucleotides are large, negatively charged, and have little resemblance to traditional small-molecule drugs-a remarkable achievement of basic and applied science. The goal of this review is to summarize the foundation underlying recent progress and describe ongoing research programs that may increase the scope and impact of oligonucleotide therapeutics.
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Affiliation(s)
- Cristina R Hofman
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- The Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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10
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Smidt JM, Lykke L, Stidsen CE, Pristovšek N, Gothelf K. Synthesis of peptide-siRNA conjugates via internal sulfonylphosphoramidate modifications and evaluation of their in vitro activity. Nucleic Acids Res 2024; 52:49-58. [PMID: 37971296 PMCID: PMC10783514 DOI: 10.1093/nar/gkad1015] [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] [Received: 07/13/2023] [Revised: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Conjugates of therapeutic oligonucleotides (ONs) including peptide conjugates, provide a potential solution to the major challenge of specific tissue delivery faced by this class of drugs. Conjugations are often positioned terminal at the ONs, although internal placement of other chemical modifications are known to be of critical importance. The introduction of internal conjugation handles in chemically modified ONs require highly specialized and expensive nucleoside phosphoramidites. Here, we present a method for synthesizing a library of peptide-siRNA conjugates by conjugation at internal phosphorous positions via sulfonylphosphoramidate modifications incorporated into the sense strand. The sulfonylphosphoramidate modification offers benefits as it can be directly incorporated into chemically modified ONs by simply changing the oxidation step during synthesis, and furthermore holds the potential to create multifunctionalized therapeutic ONs. We have developed a workflow using a novel pH-controlled amine-to-amine linker that yields peptide-siRNA conjugates linked via amide bonds, and we have synthesized conjugates between GLP1 peptides and a HPRT1 siRNA as a model system. The in vitro activity of the conjugates was tested by GLP1R activity and knockdown of the HPRT1 gene. We found that conjugation near the 3'-end is more favorable than certain central internal positions and different internal conjugation strategies were compared.
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Affiliation(s)
- Jakob Melgaard Smidt
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
| | - Lennart Lykke
- Research Chemistry, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Carsten Enggaard Stidsen
- Centre for Functional Assays and Screening, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Nuša Pristovšek
- Centre for Functional Assays and Screening, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
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11
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Sanati M, Afshari AR, Ahmadi SS, Kesharwani P, Sahebkar A. Advances in liposome-based delivery of RNA therapeutics for cancer treatment. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:177-218. [PMID: 38458738 DOI: 10.1016/bs.pmbts.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Liposomal drug delivery systems stand as versatile therapeutic platforms for precisely targeting related elements in cancerous tissues owing to their intrinsic passive and acquired active targeting capabilities and exceptional compatibility with physiologic environments. When the capacity of liposomes as nanocarriers is combined with the revolutionary potential of RNA therapies in affecting undruggable targets, the outcome would be promising drug candidates as game-changers in the cancer treatment arena. However, optimizing liposome composition, physicochemical properties, and surface chemistry is paramount to maximizing their pharmacokinetic and pharmacodynamic attributes. This review highlighted the potential of liposomes as nanovehicles for RNA therapeutics through a literature review and looked at the most recent preclinical and clinical advancements in utilizing liposomal RNA therapeutics for cancer management. Notably, the discovery of novel targets, advancements in liposome engineering, and organizing well-planned clinical trials would help uncover the incredible potential of these nanotherapeutics in cancer patients.
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Affiliation(s)
- Mehdi Sanati
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran; Experimental and Animal Study Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Amir R Afshari
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran; Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Seyed Sajad Ahmadi
- Department of Ophthalmology, Khatam-Ol-Anbia Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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12
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Neumayer C, Ng D, Requena D, Jiang CS, Qureshi A, Vaughan R, Prakash TP, Revenko A, Simon SM. GalNAc-conjugated siRNA targeting the DNAJB1-PRKACA fusion junction in fibrolamellar hepatocellular carcinoma. Mol Ther 2024; 32:140-151. [PMID: 37980543 PMCID: PMC10787139 DOI: 10.1016/j.ymthe.2023.11.012] [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: 06/15/2023] [Revised: 10/12/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023] Open
Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a rare liver cancer caused by a dominant recurrent fusion of the heat shock protein (DNAJB1) and the catalytic subunit of protein kinase A (PRKACA). Current therapies such as chemotherapy and radiation have limited efficacy, and new treatment options are needed urgently. We have previously shown that FLC tumors are dependent on the fusion kinase DNAJB1::PRKACA, making the oncokinase an ideal drug target. mRNA degrading modalities such as antisense oligonucleotides or small interfering RNAs (siRNAs) provide an opportunity to specifically target the fusion junction. Here, we identify a potent and specific siRNA that inhibits DNAJB1::PRKACA expression. We found expression of the asialoglycoprotein receptor in FLC to be maintained at sufficient levels to effectively deliver siRNA conjugated to the GalNAc ligand. We observe productive uptake and siRNA activity in FLC patient-derived xenografts (PDX) models in vitro and in vivo. Knockdown of DNAJB1::PRKACA results in durable growth inhibition of FLC PDX in vivo with no detectable toxicities. Our results suggest that this approach could be a treatment option for FLC patients.
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Affiliation(s)
- Christoph Neumayer
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Caroline S Jiang
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | - Adam Qureshi
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | - Roger Vaughan
- Hospital Biostatistics, The Rockefeller University, New York, NY, USA
| | | | | | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA.
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13
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Teodori L, Omer M, Kjems J. RNA nanostructures for targeted drug delivery and imaging. RNA Biol 2024; 21:1-19. [PMID: 38555519 PMCID: PMC10984137 DOI: 10.1080/15476286.2024.2328440] [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] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.
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Affiliation(s)
- Laura Teodori
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
| | - Marjan Omer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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14
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Belgrad J, Tang Q, Hildebrand S, Summers A, Sapp E, Echeverria D, O’Reilly D, Luu E, Bramato B, Allen S, Cooper D, Alterman J, Yamada K, Aronin N, DiFiglia M, Khvorova A. A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572404. [PMID: 38187561 PMCID: PMC10769306 DOI: 10.1101/2023.12.19.572404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Di-valent short interfering RNA (siRNA) is a promising therapeutic modality that enables sequence-specific modulation of a single target gene in the central nervous system (CNS). To treat complex neurodegenerative disorders, where pathogenesis is driven by multiple genes or pathways, di-valent siRNA must be able to silence multiple target genes simultaneously. Here we present a framework for designing unimolecular "dual-targeting" di-valent siRNAs capable of co-silencing two genes in the CNS. We reconfigured di-valent siRNA - in which two identical, linked siRNAs are made concurrently - to create linear di-valent siRNA - where two siRNAs are made sequentially attached by a covalent linker. This linear configuration, synthesized using commercially available reagents, enables incorporation of two different siRNAs to silence two different targets. We demonstrate that this dual-targeting di-valent siRNA is fully functional in the CNS of mice, supporting at least two months of maximal target silencing. Dual-targeting di-valent siRNA is highly programmable, enabling simultaneous modulation of two different disease-relevant gene pairs (e.g., Huntington's disease: MSH3 and HTT; Alzheimer's disease: APOE and JAK1) with similar potency to a mixture of single-targeting di-valent siRNAs against each gene. This work potentiates CNS modulation of virtually any pair of disease-related targets using a simple unimolecular siRNA.
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Affiliation(s)
- Jillian Belgrad
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Sam Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital; Boston, Massachusetts, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Dan O’Reilly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Eric Luu
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Sarah Allen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Julia Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
- Department of Medicine, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital; Boston, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Worcester, Massachusetts, USA
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15
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Chu Z, Zhang B, Zhou X, Yuan H, Gao C, Liu L, Xiao Y, Zhang J, Hong J, Liang J, Chen D, Yao N. A DNA/RNA heteroduplex oligonucleotide coupling asparagine depletion restricts FGFR2 fusion-driven intrahepatic cholangiocarcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102047. [PMID: 37869260 PMCID: PMC10589379 DOI: 10.1016/j.omtn.2023.102047] [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: 05/25/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
Pemigatinib, a pan-FGFR inhibitor, is approved to treat intrahepatic cholangiocarcinoma (ICC) harboring FGFR2 fusion mutations. Improving its targeting of FGFR2 fusions remains an unmet clinical need due to its pan selectivity and resistance. Here, we report a cholesterol-conjugated DNA/RNA heteroduplex oligonucleotide targeting the chimeric site in FGFR2-AHCYL1 (F-A Cho-HDO) that accumulates in ICC through endocytosis of low-density lipoprotein receptor (LDLR), which is highly expressed in both human and murine ICC. F-A Cho-HDO was determined to be a highly specific, sustainable, and well-tolerated agent for inhibiting ICC progression through posttranscriptional suppression of F-A in ICC patient-derived xenograft mouse models. Moreover, we identified an EGFR-orchestrated bypass signaling axis that partially offset the efficacy of F-A Cho-HDO. Mechanistically, EGFR-induced STAT1 upregulation promoted asparagine (Asn) synthesis through direct transcriptional upregulation of asparagine synthetase (ASNS) and dictated cell survival by preventing p53-dependent cell cycle arrest. Asn restriction with ASNase or ASNS inhibitors reduced the intracellular Asn, thereby reactivating p53 and sensitizing ICC to F-A Cho-HDO. Our findings highlight the application of genetic engineering therapies in ICC harboring FGFR2 fusions and reveal an axis of adaptation to FGFR2 inhibition that presents a rationale for the clinical evaluation of a strategy combining FGFR2 inhibitors with Asn depletion.
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Affiliation(s)
- Zhenzhen Chu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Baohuan Zhang
- Morphology Experimental Teaching Center, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xuxuan Zhou
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Hui Yuan
- Department of Gastroenterology, Huizhou Municipal Central Hospital, Huizhou, Guangdong 516001, China
| | - Chongqing Gao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Lihao Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yang Xiao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jichun Zhang
- Department of Physiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jian Hong
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Junjie Liang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Dong Chen
- Department of Pancreato-Biliary Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Nan Yao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
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16
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Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
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Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
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17
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [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: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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18
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Kumari A, Kaur A, Aggarwal G. The emerging potential of siRNA nanotherapeutics in treatment of arthritis. Asian J Pharm Sci 2023; 18:100845. [PMID: 37881798 PMCID: PMC10594572 DOI: 10.1016/j.ajps.2023.100845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/14/2023] [Accepted: 08/12/2023] [Indexed: 10/27/2023] Open
Abstract
RNA interference (RNAi) using small interfering RNA (siRNA) has shown potential as a therapeutic option for the treatment of arthritis by silencing specific genes. However, siRNA delivery faces several challenges, including stability, targeting, off-target effects, endosomal escape, immune response activation, intravascular degradation, and renal clearance. A variety of nanotherapeutics like lipidic nanoparticles, liposomes, polymeric nanoparticles, and solid lipid nanoparticles have been developed to improve siRNA cellular uptake, protect it from degradation, and enhance its therapeutic efficacy. Researchers are also investigating chemical modifications and bioconjugation to reduce its immunogenicity. This review discusses the potential of siRNA nanotherapeutics as a therapeutic option for various immune-mediated diseases, including rheumatoid arthritis, osteoarthritis, etc. siRNA nanotherapeutics have shown an upsurge of interest and the future looks promising for such interdisciplinary approach-based modalities that combine the principles of molecular biology, nanotechnology, and formulation sciences.
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Affiliation(s)
- Anjali Kumari
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Amanpreet Kaur
- Centre for Advanced Formulation Technology, Delhi Pharmaceutical Sciences and Research, New Delhi 110017, India
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Geeta Aggarwal
- Centre for Advanced Formulation Technology, Delhi Pharmaceutical Sciences and Research, New Delhi 110017, India
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
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19
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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20
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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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21
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Oshchepkova A, Zenkova M, Vlassov V. Extracellular Vesicles for Therapeutic Nucleic Acid Delivery: Loading Strategies and Challenges. Int J Mol Sci 2023; 24:ijms24087287. [PMID: 37108446 PMCID: PMC10139028 DOI: 10.3390/ijms24087287] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane vesicles released into the extracellular milieu by cells of various origins. They contain different biological cargoes, protecting them from degradation by environmental factors. There is an opinion that EVs have a number of advantages over synthetic carriers, creating new opportunities for drug delivery. In this review, we discuss the ability of EVs to function as carriers for therapeutic nucleic acids (tNAs), challenges associated with the use of such carriers in vivo, and various strategies for tNA loading into EVs.
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Affiliation(s)
- Anastasiya Oshchepkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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22
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Uddin N, Binzel DW, Shu D, Fu TM, Guo P. Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome. Acta Pharm Sin B 2023; 13:1383-1399. [PMID: 37139430 PMCID: PMC10149909 DOI: 10.1016/j.apsb.2022.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Exosome is an excellent vesicle for in vivo delivery of therapeutics, including RNAi and chemical drugs. The extremely high efficiency in cancer regression can partly be attributed to its fusion mechanism in delivering therapeutics to cytosol without endosome trapping. However, being composed of a lipid-bilayer membrane without specific recognition capacity for aimed-cells, the entry into nonspecific cells can lead to potential side-effects and toxicity. Applying engineering approaches for targeting-capacity to deliver therapeutics to specific cells is desirable. Techniques with chemical modification in vitro and genetic engineering in cells have been reported to decorate exosomes with targeting ligands. RNA nanoparticles have been used to harbor tumor-specific ligands displayed on exosome surface. The negative charge reduces nonspecific binding to vital cells with negatively charged lipid-membrane due to the electrostatic repulsion, thus lowering the side-effect and toxicity. In this review, we focus on the uniqueness of RNA nanoparticles for exosome surface display of chemical ligands, small peptides or RNA aptamers, for specific cancer targeting to deliver anticancer therapeutics, highlighting recent advances in targeted delivery of siRNA and miRNA that overcomes the previous RNAi delivery roadblocks. Proper understanding of exosome engineering with RNA nanotechnology promises efficient therapies for a wide range of cancer subtypes.
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Affiliation(s)
- Nasir Uddin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Daniel W. Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry & Pharmacology, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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23
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Zhang H, Kelly K, Lee J, Echeverria D, Cooper D, Panwala R, Chen Z, Gaston N, Newby GA, Xie J, Liu DR, Gao G, Wolfe SA, Khvorova A, Watts JK, Sontheimer EJ. Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533459. [PMID: 36993169 PMCID: PMC10055305 DOI: 10.1101/2023.03.20.533459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a "protecting oligo"), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.
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Affiliation(s)
- Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - David Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Rebecca Panwala
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02139, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02139, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02139, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Scot A. Wolfe
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
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24
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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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25
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Jeon T, Luther DC, Goswami R, Bell C, Nagaraj H, Anil Cicek Y, Huang R, Mas-Rosario JA, Elia JL, Im J, Lee YW, Liu Y, Scaletti F, Farkas ME, Mager J, Rotello VM. Engineered Polymer-siRNA Polyplexes Provide Effective Treatment of Lung Inflammation. ACS NANO 2023; 17:4315-4326. [PMID: 36802503 PMCID: PMC10627429 DOI: 10.1021/acsnano.2c08690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Uncontrolled inflammation is responsible for acute and chronic diseases in the lung. Regulating expression of pro-inflammatory genes in pulmonary tissue using small interfering RNA (siRNA) is a promising approach to combatting respiratory diseases. However, siRNA therapeutics are generally hindered at the cellular level by endosomal entrapment of delivered cargo and at the organismal level by inefficient localization in pulmonary tissue. Here we report efficient anti-inflammatory activity in vitro and in vivo using polyplexes of siRNA and an engineered cationic polymer (PONI-Guan). PONI-Guan/siRNA polyplexes efficiently deliver siRNA cargo to the cytosol for highly efficient gene knockdown. Significantly, these polyplexes exhibit inherent targeting to inflamed lung tissue following intravenous administration in vivo. This strategy achieved effective (>70%) knockdown of gene expression in vitro and efficient (>80%) silencing of TNF-α expression in lipopolysaccharide (LPS)-challenged mice using a low (0.28 mg/kg) siRNA dosage.
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Affiliation(s)
- Taewon Jeon
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - David C. Luther
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Ritabrita Goswami
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Charlotte Bell
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Harini Nagaraj
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Yagiz Anil Cicek
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Rui Huang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Javier A. Mas-Rosario
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA
| | - James L. Elia
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Jungkyun Im
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
- Department of Chemical Engineering, and Department of Electronic Materials, Devices, and Equipment Engineering, Soonchunhyang University, 22 Soonchunhyangro, Asan, 31538, Republic of Korea
| | - Yi-Wei Lee
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Yuanchang Liu
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Federica Scaletti
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Michelle E. Farkas
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N Pleasant Street, Amherst, Massachusetts, 01003, USA
| | - Vincent M. Rotello
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, Massachusetts, 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts, 01003, USA
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26
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Fernandez C, Giorgees I, Goss E, Desaulniers JP. Effective carrier-free gene-silencing activity of sphingosine-modified siRNAs. Org Biomol Chem 2023; 21:2107-2117. [PMID: 36645381 DOI: 10.1039/d2ob02099h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA interference (RNAi) is a natural cellular process that silences the expression of target genes in a sequence-specific way by mediating targeted mRNA degradation. One of the main challenges in RNAi research is developing an effective career-free delivery system and targeting cells in the central nervous system (CNS). Recently, lipid-conjugated systems involving fatty acids have shown promising potential as safe and effective delivery systems of oligonucleotides to CNS cells due to their hydrophobic tails and interactions with the cell's hydrophobic membrane. Therefore, in this study, we are interested in creating career-free siRNA therapeutics for potential applications in drug delivery to the CNS. Here we explore different synthetic pathways of conjugating sphingolipids containing long-carbon chains to siRNA and assess their effectiveness as career-free delivery systems. In this project, a library of sphingosine-modified siRNAs was created, and their gene-silencing effect was evaluated in both the presence and absence of a transfection carrier. siRNAs modified with one or two sphingosine moieties resulted in dose-dependent gene knockdown while demonstrating promising results for their use as carrier-free agents. The IC50 values of single-modified siRNAs ranged from 49.9 nM to 670.7 nM, whereas double-modified siRNAs had IC50 values in the range of 49.9 nM to 66.4 nM. In conclusion, sphingosine-modified siRNAs show promising results in advancing carrier-free siRNA therapeutics.
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Affiliation(s)
- Charlene Fernandez
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Ifrodet Giorgees
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
| | - Eva Goss
- Synthose Inc., 50 Viceroy Road Unit 7, Concord, Ontario, L4K 3A7 Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1G 0C5, Canada.
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27
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Modified Linear Peptides Effectively Silence STAT-3 in Breast Cancer and Ovarian Cancer Cell Lines. Pharmaceutics 2023; 15:pharmaceutics15020666. [PMID: 36839988 PMCID: PMC9962452 DOI: 10.3390/pharmaceutics15020666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
RNA interference (RNAi) has drawn enormous attention as a powerful tool because of its capability to interfere with mRNA and protein production. However, designing a safe and efficient delivery system in RNAi therapeutics remains challenging. Herein, we have designed and synthesized several linear peptides containing tryptophan (W) and arginine (R) residues separated by the β-alanine (βA) spacer and attached to a lipophilic fatty acyl chain, cholesterol, or PEG. The peptide backbone sequences were: Ac-C-βA-βA-W4-βA-βA-R4-CO-NH2 and Ac-K-βA-βA-W4-βA-βA-R4-CO-NH2, with only a difference in N-terminal amino acid. The cysteine side chain in the first sequence was used for the conjugation with PEG2000 and PEG550. Alternatively, the side chain of lysine in the second sequence was used for conjugation with cholesterol or oleic acid. We hypothesized that amphiphilic peptides and optimum fatty acyl chain or PEG could function as an effective siRNA carrier by complementing each structural component's self-assembly and membrane internalization properties. None of the designed peptides showed cytotoxicity up to 10 µM. Serum stability studies suggested that the newly designed peptides efficiently protected siRNA against early degradation by nucleases. Flow cytometry analysis indicated 50-90% cellular uptake of siRNA using the newly developed modified linear peptides (MLPs). Western blot results revealed more than 90% protein downregulation after targeting STAT3 in MDA-MB-231 and SKOV-3 cell lines. In summary, a new peptide class was developed to safely and efficiently deliver siRNA.
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28
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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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29
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Engelbeen S, Pasteuning-Vuhman S, Boertje-van der Meulen J, Parmar R, Charisse K, Sepp-Lorenzino L, Manoharan M, Aartsma-Rus A, van Putten M. Efficient Downregulation of Alk4 in Skeletal Muscle After Systemic Treatment with Conjugated siRNAs in a Mouse Model for Duchenne Muscular Dystrophy. Nucleic Acid Ther 2023; 33:26-34. [PMID: 36269327 PMCID: PMC9940804 DOI: 10.1089/nat.2022.0021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Downregulation of genes involved in the secondary pathology of Duchenne muscular dystrophy, for example, inflammation, fibrosis, and adiposis, is an interesting approach to ameliorate degeneration of muscle and replacement by fibrotic and adiposis tissue. Small interfering RNAs (siRNAs) are able to downregulate target genes, however, delivery of siRNAs to skeletal muscle still remains a challenge. We investigated delivery of fully chemically modified, cholesterol-conjugated siRNAs targeting Alk4, a nontherapeutic target that is expressed highly in muscle. We observed that a single intravenous or intraperitoneal (IP) injection of 10 mg/kg resulted in significant downregulation of Alk4 mRNA expression in skeletal muscles in both wild-type and mdx mice. Treatment with multiple IP injections of 10 mg/kg led to an overall reduction of Alk4 expression, reaching significance in tibialis anterior (39.7% ± 6.2%), diaphragm (32.7% ± 5.8%), and liver (41.3% ± 29.9%) in mdx mice. Doubling of the siRNA dose did not further increase mRNA silencing in muscles of mdx mice. The chemically modified conjugated siRNAs used in this study are very promising for delivery to both nondystrophic and dystrophic muscles and could have major implications for treatment of muscular dystrophy pathology.
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Affiliation(s)
- Sarah Engelbeen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Rubina Parmar
- Alnalym Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | | | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike van Putten
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,Address correspondence to: Maaike van Putten, PhD, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
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30
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Fàbrega C, Aviñó A, Navarro N, Jorge AF, Grijalvo S, Eritja R. Lipid and Peptide-Oligonucleotide Conjugates for Therapeutic Purposes: From Simple Hybrids to Complex Multifunctional Assemblies. Pharmaceutics 2023; 15:pharmaceutics15020320. [PMID: 36839642 PMCID: PMC9959333 DOI: 10.3390/pharmaceutics15020320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Antisense and small interfering RNA (siRNA) oligonucleotides have been recognized as powerful therapeutic compounds for targeting mRNAs and inducing their degradation. However, a major obstacle is that unmodified oligonucleotides are not readily taken up into tissues and are susceptible to degradation by nucleases. For these reasons, the design and preparation of modified DNA/RNA derivatives with better stability and an ability to be produced at large scale with enhanced uptake properties is of vital importance to improve current limitations. In the present study, we review the conjugation of oligonucleotides with lipids and peptides in order to produce oligonucleotide conjugates for therapeutics aiming to develop novel compounds with favorable pharmacokinetics.
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Affiliation(s)
- Carme Fàbrega
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Anna Aviñó
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Natalia Navarro
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Andreia F. Jorge
- Department of Chemistry, Coimbra Chemistry Centre (CQC), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Santiago Grijalvo
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Colloidal and Interfacial Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Correspondence: ; Tel.: +34-934006145
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31
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Kurtzhals P, Østergaard S, Nishimura E, Kjeldsen T. Derivatization with fatty acids in peptide and protein drug discovery. Nat Rev Drug Discov 2023; 22:59-80. [PMID: 36002588 DOI: 10.1038/s41573-022-00529-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 01/28/2023]
Abstract
Peptides and proteins are widely used to treat a range of medical conditions; however, they often have to be injected and their effects are short-lived. These shortcomings of the native structure can be addressed by molecular engineering, but this is a complex undertaking. A molecular engineering technology initially applied to insulin - and which has now been successfully applied to several biopharmaceuticals - entails the derivatization of peptides and proteins with fatty acids. Various protraction mechanisms are enabled by the specific characteristics and positions of the attached fatty acid. Furthermore, the technology can ensure a long half-life following oral administration of peptide drugs, can alter the distribution of peptides and may hold potential for tissue targeting. Due to the inherent safety and well-defined chemical nature of the fatty acids, this technology provides a versatile approach to peptide and protein drug discovery.
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32
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Craig K, Abrams M, Amiji M. Cholesterol-Conjugated siRNA Silencing Tnf for the Treatment of Liver Macrophage-Mediated Acute Inflammation in Nonalcoholic Fatty Liver Disease. Nucleic Acid Ther 2023; 33:35-44. [PMID: 36318487 DOI: 10.1089/nat.2022.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite wide recognition as a disease of pandemic proportions, effective treatments for nonalcoholic fatty liver disease (NAFLD) remain elusive. Most of the current clinical programs aim to reduce hepatic fat accumulation and, thus, prevent downstream inflammation and fibrosis. To date, this therapeutic approach has helped identify a potential disconnect between steatosis reduction and disease resolution. Mounting preclinical evidence indicates liver inflammation may play a major role in steatosis development and fibrosis but has not garnered the same clinical representation. This may be owing to deficiencies in standard therapeutic modalities that limit their application in NAFLD. RNA interference (RNAi) is an attractive approach to targeting liver inflammation owing to its clinical safety profile, target specificity, and limited biodistribution. In this study, we characterize a simple cholesterol-short-interfering RNA (siRNA) conjugate system targeting Tnf mRNA in liver macrophages for the treatment of NAFLD. First, we observed delivery and anti-inflammatory activity in an acute liver inflammation model. In a follow-up murine NAFLD model, we observed total prevention of nearly all hallmarks of this disease: steatosis, inflammation, and fibrosis. This simple conjugate siRNA delivery system may be the first to show RNAi activity in liver macrophages and provide evidence for a novel therapeutic approach to inflammation in NAFLD.
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Affiliation(s)
- Kevin Craig
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, Massachusetts, USA.,Department of Discovery Research, Dicerna Pharmaceuticals, Inc., Lexington, Massachusetts, USA
| | - Marc Abrams
- Department of Discovery Research, Dicerna Pharmaceuticals, Inc., Lexington, Massachusetts, USA
| | - Mansoor Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, Massachusetts, USA.,Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, Massachusetts, USA
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33
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Lee JW, Choi J, Choi Y, Kim K, Yang Y, Kim SH, Yoon HY, Kwon IC. Molecularly engineered siRNA conjugates for tumor-targeted RNAi therapy. J Control Release 2022; 351:713-726. [DOI: 10.1016/j.jconrel.2022.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/28/2022]
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34
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Investigation of the ionic conditions in SiRNA-mediated delivery through its carriers in the cell membrane: a molecular dynamic simulation. Sci Rep 2022; 12:17520. [PMID: 36266467 PMCID: PMC9582388 DOI: 10.1038/s41598-022-22509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023] Open
Abstract
SiRNA is a new generation of drug molecules and a new approach for treating a variety of diseases such as cancer and viral infections. SiRNA delivery to cells and translocation into cytoplasm are the main challenges in the clinical application of siRNA. Lipid carriers are one of the most successful carriers for siRNA delivery. In this study, we investigated the interaction of siRNA with a zwitterionic bilayer and how ion concentration and lipid conjugation can affect it. The divalent cation such as Mg2+ ions could promote the siRNA adsorption on the bilayer surface. The cation ions can bind to the head groups of lipids and the grooves of siRNA molecules and form bridges between the siRNA and bilayer surface. Our findings demonstrated the bridges formed by divalent ions could facilitate the attachment of siRNA to the membrane surface. We showed that the divalent cations can regulate the bridging-driven membrane attachment and it seems the result of this modulation can be used for designing biomimetic devices. In the following, we examined the effect of cations on the interaction between siRNA modified by cholesterol and the membrane surface. Our MD simulations showed that in the presence of Mg2+, the electrostatic and vdW energy between the membrane and siRNA were higher compared to those in the presence of NA+. We showed that the electrostatic interaction between membrane and siRNA cannot be facilitated only by cholesterol conjugated. Indeed, cations are essential to create coulomb repulsion and enable membrane attachment. This study provides important insight into liposome carriers for siRNA delivery and could help us in the development of siRNA-based therapeutics. Due to the coronavirus pandemic outbreak, these results may shed light on the new approach for treating these diseases and their molecular details.
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35
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Thakur S, Sinhari A, Jain P, Jadhav HR. A perspective on oligonucleotide therapy: Approaches to patient customization. Front Pharmacol 2022; 13:1006304. [PMID: 36339619 PMCID: PMC9626821 DOI: 10.3389/fphar.2022.1006304] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 09/12/2023] Open
Abstract
It is estimated that the human genome encodes 15% of proteins that are considered to be disease-modifying. Only 2% of these proteins possess a druggable site that the approved clinical candidates target. Due to this disparity, there is an immense need to develop therapeutics that may better mitigate the disease or disorders aroused by non-druggable and druggable proteins or enzymes. The recent surge in approved oligonucleotide therapeutics (OT) indicates the imminent potential of these therapies. Oligonucleotide-based therapeutics are of intermediate size with much-improved selectivity towards the target and fewer off-target effects than small molecules. The OTs include Antisense RNAs, MicroRNA (MIR), small interfering RNA (siRNA), and aptamers, which are currently being explored for their use in neurodegenerative disorders, cancer, and even orphan diseases. The present review is a congregated effort to present the past and present of OTs and the current efforts to make OTs for plausible future therapeutics. The review provides updated literature on the challenges and bottlenecks of OT and recent advancements in OT drug delivery. Further, this review deliberates on a newly emerging approach to personalized treatment for patients with rare and fatal diseases with OT.
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Affiliation(s)
- Shikha Thakur
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
| | - Apurba Sinhari
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Hemant R. Jadhav
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
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36
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Tang X, Liang Y, Sun G, He Q, Hou Z, Jiang X, Gao P, Qu H. Upregulation of CRABP2 by TET1-mediated DNA hydroxymethylation attenuates mitochondrial apoptosis and promotes oxaliplatin resistance in gastric cancer. Cell Death Dis 2022; 13:848. [PMID: 36195596 PMCID: PMC9532395 DOI: 10.1038/s41419-022-05299-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022]
Abstract
Oxaliplatin is the main chemotherapy drug for gastric cancer (GC), but quite a few patients are resistant to oxaliplatin, which contributes to the poor prognosis of GC patients. There is therefore an urgent need to identify potential targets for reversing chemotherapy resistance in GC patients. In this study, we analyzed the tumor samples of GC patients who received neoadjuvant chemotherapy based on oxaliplatin through quantitative proteomics and identified the potential chemoresistance-related protein cellular retinoic acid binding protein 2 (CRABP2). CRABP2 was significantly upregulated in the tumor tissues of chemoresistant GC patients and was closely related to prognosis. The results of cell function experiments showed that CRABP2 can promote the oxaliplatin resistance of GC cells in vitro. Coimmunoprecipitation and GST pulldown assays showed that CRAPB2 expedited the binding of BAX and PARKIN in GC cells and facilitated the ubiquitination-mediated degradation of BAX. Furthermore, both the in vitro assay and cell-derived xenograft (CDX) in vivo model verified that CRABP2 promoted oxaliplatin resistance by inhibiting BAX-dependent cell apoptosis. Further experiments proved that the abnormally high expression of CRABP2 in oxaliplatin-resistant GC cells was affected by TET1-mediated DNA hydroxymethylation. The patient-derived xenograft (PDX) model suggested that interference with CRABP2 reversed oxaliplatin resistance in GC in vivo. In conclusion, the results of our study show that CRABP2 was a key molecule in oxaliplatin resistance regulation and could be a new target for reversing the chemoresistance of GC.
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Affiliation(s)
- Xiaolong Tang
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Yahang Liang
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Guorui Sun
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Qingsi He
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Zhenyu Hou
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Xingzhi Jiang
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Peng Gao
- grid.452402.50000 0004 1808 3430Department of Pathology, Qilu Hospital of Shandong University, Jinan, 250012 China
| | - Hui Qu
- grid.452402.50000 0004 1808 3430Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012 China
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37
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Engineered ionizable lipid siRNA conjugates enhance endosomal escape but induce toxicity in vivo. J Control Release 2022; 349:831-843. [PMID: 35917865 DOI: 10.1016/j.jconrel.2022.07.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022]
Abstract
Lipid conjugation supports delivery of small interfering RNAs (siRNAs) to extrahepatic tissues, expanding the therapeutic potential of siRNAs beyond liver indications. However, siRNA silencing efficacy in extrahepatic tissues remains inferior to that routinely achieved in liver, partially due to the low rate of endosomal escape following siRNA internalization. Improving siRNA endosomal release into cytoplasm is crucial to improving efficacy of lipid-conjugated siRNAs. Given the ability of ionizable lipids to enhance endosomal escape in a context of lipid nanoparticles (LNP), here, we provide the first report on the effect of an ionizable lipid conjugate on siRNA endosomal escape, tissue distribution, efficacy, and toxicity in vivo. After developing a synthetic route to covalently attach the ionizable lipid, DLin-MC3-DMA, to siRNAs, we demonstrate that DLin-MC3-DMA enhances endosomal escape in cell culture without compromising siRNA efficacy. In mice, DLin-MC3-DMA conjugated siRNAs exhibit a similar overall tissue distribution profile to the similarly hydrophobic cholesterol-conjugated siRNA. However, only DLin-MC3-DMA conjugated siRNAs accumulated in vascular compartments, suggesting an effect of conjugate structure on intratissue distribution. Interestingly, we observed non-specific modulation of gene expression in tissues with high accumulation of DLin-MC3-DMA siRNAs (>20 pmol/mg of tissue) while limited non-specific gene modulation has been observed in tissues with lower siRNA accumulation. These findings suggest modulating the nature of the conjugate is a promising strategy to alter siRNA intratissue and intracellular trafficking. Fine-tuning the nature of the conjugate to optimize endosomal escape while minimizing toxicity will be critical for the progression of therapeutic siRNA applications beyond the liver.
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38
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Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
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39
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Madaoui M, Datta D, Wassarman K, Zlatev I, Egli M, Ross BS, Manoharan M. A Chemical Approach to Introduce 2,6-Diaminopurine and 2-Aminoadenine Conjugates into Oligonucleotides without Need for Protecting Groups. Org Lett 2022; 24:6111-6116. [PMID: 35973215 PMCID: PMC9425559 DOI: 10.1021/acs.orglett.2c01848] [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] [Indexed: 11/28/2022]
Abstract
![]()
We report a simple, postsynthetic strategy for synthesis
of oligonucleotides
containing 2,6-diaminopurine nucleotides and 2-aminoadenine conjugates
using 2-fluoro-6-amino-adenosine. The strategy allows introduction
of 2,6-diaminopurine and other 2-amino group-containing ligands. The
strongly electronegative 2-fluoro deactivates 6-NH2 obviating
the need for any protecting group on adenine, and simple aromatic
nucleophilic substitution of fluorine makes reaction with aqueous
NH3 or R-NH2 feasible at the 2-position.
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Affiliation(s)
- Mimouna Madaoui
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Bruce S Ross
- Ross Chemistry Consulting, El Granada, California 94018, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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40
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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: 14] [Impact Index Per Article: 7.0] [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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41
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Datta D, Mori S, Madaoui M, Wassarman K, Zlatev I, Manoharan M. Aminooxy Click Chemistry as a Tool for Bis-homo and Bis-hetero Ligand Conjugation to Nucleic Acids. Org Lett 2022; 24:4496-4501. [PMID: 35715221 PMCID: PMC9251770 DOI: 10.1021/acs.orglett.2c00988] [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] [Indexed: 11/30/2022]
Abstract
![]()
An aminooxy click
chemistry (AOCC) strategy was used to synthesize
nucleoside building blocks for incorporation during solid-support
synthesis of oligonucleotides to enable bis-homo and bis-hetero conjugation
of various biologically relevant ligands. The bis-homo aminooxy conjugation
leads to bivalent ligand presentation, whereas the bis-hetero conjugation
allows the placement of different ligands with either the same or
different chemical linkages. This facile synthetic methodology allows
introduction of two different ligands with different biological functions
simultaneously.
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Affiliation(s)
- Dhrubajyoti Datta
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Shohei Mori
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Mimouna Madaoui
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Kelly Wassarman
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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Humphreys SC, Davis JA, Iqbal S, Kamel A, Kulmatycki K, Lao Y, Liu X, Rodgers J, Snoeys J, Vigil A, Weng Y, Wiethoff CM, Wittwer MB. Considerations and recommendations for assessment of plasma protein binding and drug-drug interactions for siRNA therapeutics. Nucleic Acids Res 2022; 50:6020-6037. [PMID: 35687098 PMCID: PMC9226521 DOI: 10.1093/nar/gkac456] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/25/2022] [Accepted: 06/06/2022] [Indexed: 11/12/2022] Open
Abstract
At the time of writing, although siRNA therapeutics are approved for human use, no official regulatory guidance specific to this modality is available. In the absence of guidance, preclinical development for siRNA followed a hybrid of the small molecule and biologics guidance documents. However, siRNA differs significantly from small molecules and protein-based biologics in its physicochemical, absorption, distribution, metabolism and excretion properties, and its mechanism of action. Consequently, certain reports typically included in filing packages for small molecule or biologics may benefit from adaption, or even omission, from an siRNA filing. In this white paper, members of the 'siRNA working group' in the IQ Consortium compile a list of reports included in approved siRNA filing packages and discuss the relevance of two in vitro reports-the plasma protein binding evaluation and the drug-drug interaction risk assessment-to support siRNA regulatory filings. Publicly available siRNA approval packages and the literature were systematically reviewed to examine the role of siRNA plasma protein binding and drug-drug interactions in understanding pharmacokinetic/pharmacodynamic relationships, safety and translation. The findings are summarized into two decision trees to help guide industry decide when in vitro siRNA plasma protein binding and drug-drug interaction studies are warranted.
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Affiliation(s)
| | - John A Davis
- PKS Department, Novartis, Cambridge, MA 02139, USA
| | | | - Amin Kamel
- Global DMPK, Takeda, San Diego, CA 92121, USA
| | | | - Yanbin Lao
- DMPK, Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Xiumin Liu
- Early Development, Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Rodgers
- PKDM Department, Amgen Inc., South San Francisco, CA 94080, USA
| | - Jan Snoeys
- DMPK Department, Janssen R&D, Beerse 2340, Belgium
| | - Adam Vigil
- DMPK, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT 06877, USA
| | - Yan Weng
- Early Clinical Development Clinical Pharmacology Department, Pfizer, Cambridge, MA 02139, USA
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Brown KM, Nair JK, Janas MM, Anglero-Rodriguez YI, Dang LTH, Peng H, Theile CS, Castellanos-Rizaldos E, Brown C, Foster D, Kurz J, Allen J, Maganti R, Li J, Matsuda S, Stricos M, Chickering T, Jung M, Wassarman K, Rollins J, Woods L, Kelin A, Guenther DC, Mobley MW, Petrulis J, McDougall R, Racie T, Bombardier J, Cha D, Agarwal S, Johnson L, Jiang Y, Lentini S, Gilbert J, Nguyen T, Chigas S, LeBlanc S, Poreci U, Kasper A, Rogers AB, Chong S, Davis W, Sutherland JE, Castoreno A, Milstein S, Schlegel MK, Zlatev I, Charisse K, Keating M, Manoharan M, Fitzgerald K, Wu JT, Maier MA, Jadhav V. Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates. Nat Biotechnol 2022; 40:1500-1508. [PMID: 35654979 DOI: 10.1038/s41587-022-01334-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/22/2022] [Indexed: 01/03/2023]
Abstract
Therapeutics based on short interfering RNAs (siRNAs) delivered to hepatocytes have been approved, but new delivery solutions are needed to target additional organs. Here we show that conjugation of 2'-O-hexadecyl (C16) to siRNAs enables safe, potent and durable silencing in the central nervous system (CNS), eye and lung in rodents and non-human primates with broad cell type specificity. We show that intrathecally or intracerebroventricularly delivered C16-siRNAs were active across CNS regions and cell types, with sustained RNA interference (RNAi) activity for at least 3 months. Similarly, intravitreal administration to the eye or intranasal administration to the lung resulted in a potent and durable knockdown. The preclinical efficacy of an siRNA targeting the amyloid precursor protein was evaluated through intracerebroventricular dosing in a mouse model of Alzheimer's disease, resulting in amelioration of physiological and behavioral deficits. Altogether, C16 conjugation of siRNAs has the potential for safe therapeutic silencing of target genes outside the liver with infrequent dosing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jing Li
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | | | - Alex Kelin
- Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | | | | | | | | | | | - Diana Cha
- Alnylam Pharmaceuticals, Cambridge, MA, USA
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Diener C, Keller A, Meese E. Emerging concepts of miRNA therapeutics: from cells to clinic. Trends Genet 2022; 38:613-626. [PMID: 35303998 DOI: 10.1016/j.tig.2022.02.006] [Citation(s) in RCA: 247] [Impact Index Per Article: 123.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are very powerful genetic regulators, as evidenced by the fact that a single miRNA can direct entire cellular pathways via interacting with a broad spectrum of target genes. This property renders miRNAs as highly interesting therapeutic tools to restore cell functions that are altered as part of a disease phenotype. However, this strength of miRNAs is also a weakness because their cellular effects are so numerous that off-target effects can hardly be avoided. In this review, we point out the main challenges and the strategies to specifically address the problems that need to be surmounted in the push toward a therapeutic application of miRNAs. Particular emphasis is given to approaches that have already found their way into clinical studies.
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Affiliation(s)
- Caroline Diener
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Center for Bioinformatics, Medical Faculty, Saarland University, 66123 Saarbrücken, Germany; Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, Stanford, CA 94305, USA.
| | - Eckart Meese
- Institute of Human Genetics, Medical Faculty, Saarland University, 66421 Homburg, Germany
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Tsujimoto R, Yurube T, Takeoka Y, Kanda Y, Miyazaki K, Ohnishi H, Kakiuchi Y, Miyazaki S, Zhang Z, Takada T, Kuroda R, Kakutani K. Involvement of autophagy in the maintenance of rat intervertebral disc homeostasis: an in-vitro and in-vivo RNA interference study of Atg5. Osteoarthritis Cartilage 2022; 30:481-493. [PMID: 34958937 DOI: 10.1016/j.joca.2021.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE In the largest avascular low-nutrient intervertebral disc, resident cells would utilize autophagy, a stress-response survival mechanism by self-digestion and recycling wastes. Our goal was to elucidate the involvement of autophagy in disc homeostasis through RNA interference of autophagy-related gene 5 (Atg5). DESIGN In vitro, small interfering RNAs (siRNAs) targeting autophagy-essential Atg5 were transfected into rat disc cells. Cell viability with levels of autophagy including Atg5 expression, apoptosis, and senescence was assessed under serum starvation and/or pro-inflammatory interleukin-1 beta (IL-1β) stimulation. In vivo, time-course autophagic flux was monitored following Alexa Fluor® 555-labeled Atg5-siRNA injection into rat tail discs. Furthermore, 24-h temporary static compression-induced disruption of Atg5 siRNA-injected discs was observed by radiography, histomorphology, and immunofluorescence. RESULTS In disc cells, three different Atg5 siRNAs consistently suppressed autophagy with Atg5 protein knockdown (mean 44.4% [95% confidence interval: -51.7, -37.1], 51.5% [-80.5, -22.5], 62.3% [-96.6, -28.2]). Then, Atg5 knockdown reduced cell viability through apoptosis and senescence not in serum-supplemented medium (93.6% [-0.8, 21.4]) but in serum-deprived medium (66.4% [-29.8, -8.6]) further with IL-1β (44.5% [-36.9, -23.5]). In disc tissues, immunofluorescence detected intradiscal signals for the labeled siRNA even at 56-d post-injection. Immunoblotting found 56-d autophagy suppression with prolonged Atg5 knockdown (33.2% [-52.8, -5.3]). With compression, Atg5 siRNA-injected discs presented radiographic height loss ([-43.9, -0.8]), histological damage ([-5.5, -0.2]), and immunofluorescent apoptosis ([2.2, 22.2]) and senescence ([4.1, 19.9]) induction compared to control siRNA-injected discs at 56 d. CONCLUSIONS This loss-of-function study suggests Atg5-dependent autophagy-mediated anti-apoptosis and anti-senescence. Autophagy could be a molecular therapeutic target for degenerative disc disease.
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Affiliation(s)
- R Tsujimoto
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - T Yurube
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Y Takeoka
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Y Kanda
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - K Miyazaki
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - H Ohnishi
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Y Kakiuchi
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - S Miyazaki
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - Z Zhang
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - T Takada
- Department of Orthopaedic Surgery, Kobe Hokuto Hospital, 37-3 Yamada-cho Shimotanigami Aza Umekidani, Kita-ku, Kobe, 651-1243, Japan.
| | - R Kuroda
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
| | - K Kakutani
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.
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Therapeutic RNA-silencing oligonucleotides in metabolic diseases. Nat Rev Drug Discov 2022; 21:417-439. [PMID: 35210608 DOI: 10.1038/s41573-022-00407-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Recent years have seen unprecedented activity in the development of RNA-silencing oligonucleotide therapeutics for metabolic diseases. Improved oligonucleotide design and optimization of synthetic nucleic acid chemistry, in combination with the development of highly selective and efficient conjugate delivery technology platforms, have established and validated oligonucleotides as a new class of drugs. To date, there are five marketed oligonucleotide therapies, with many more in clinical studies, for both rare and common liver-driven metabolic diseases. Here, we provide an overview of recent developments in the field of oligonucleotide therapeutics in metabolism, review past and current clinical trials, and discuss ongoing challenges and possible future developments.
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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Deprey K, Batistatou N, Debets MF, Godfrey J, VanderWall KB, Miles RR, Shehaj L, Guo J, Andreucci A, Kandasamy P, Lu G, Shimizu M, Vargeese C, Kritzer JA. Quantitative Measurement of Cytosolic and Nuclear Penetration of Oligonucleotide Therapeutics. ACS Chem Biol 2022; 17:348-360. [PMID: 35034446 PMCID: PMC9252293 DOI: 10.1021/acschembio.1c00830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major obstacle in the development of effective oligonucleotide therapeutics is a lack of understanding about their cytosolic and nuclear penetration. To address this problem, we have applied the chloroalkane penetration assay (CAPA) to oligonucleotide therapeutics. CAPA was used to quantitate cytosolic delivery of antisense oligonucleotides (ASOs) and siRNAs and to explore the effects of a wide variety of commonly used chemical modifications and their patterning. We evaluated potential artifacts by exploring the effects of serum, comparing activity data and CAPA data, and assessing the impact of the chloroalkane tag and its linker chemistry. We also used viral transduction to expand CAPA to the nuclear compartment in epithelial and neuronal cell lines. Using this enhanced method, we measured a 48-h time course of nuclear penetration for a panel of chemically diverse modified RNAs. Moving forward, CAPA will be a useful tool for deconvoluting the complex processes of endosomal uptake, escape into the cytosol, and subcellular trafficking of oligonucleotide therapeutics in therapeutically relevant cell types.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marjoke F. Debets
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Jack Godfrey
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Kirstin B. VanderWall
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rebecca R. Miles
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Livia Shehaj
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiaxing Guo
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Amy Andreucci
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | | | - Genliang Lu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Mamoru Shimizu
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Chandra Vargeese
- Wave Life Sciences, Cambridge, Massachusetts 02138, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States,corresponding author:
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Liu X, Ding F, Guo Y, Jiang K, Fu Y, Zhu L, Li M, Zhu X, Zhang C. Complexing the Pre-assembled Brush-like siRNA with Poly(β-amino ester) for Efficient Gene Silencing. ACS APPLIED BIO MATERIALS 2022; 5:1857-1867. [PMID: 35107256 DOI: 10.1021/acsabm.1c01182] [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: 11/29/2022]
Abstract
Small interfering RNA (siRNA) has been emerging as a highly selective and effective pharmaceutics for treating broad classes of diseases. However, the practical application of siRNA agent is often hampered by its poor crossing of the cellular membrane barrier and ineffective releasing from endosome to cytoplasm, leading to low gene silencing efficacy for clinical purposes. Thus far, cationic lipid and polymer-based vectors have been extensively explored for gene delivery. Yet condensing the rigid and highly negatively charged siRNA duplex to form a stable complex vehicle usually requires a large load of cationic carriers, prone to raising the toxicity issue for delivery. Herein, we develop a simple strategy that can efficiently condense the siRNAs into nanoparticle vehicles for target gene regulation. In this approach, we first employ a DNA-grafted polycaprolactone (DNA-g-PCL) brush as template to organize the small rigid siRNAs into a large brush-like structure (siRNA-brush) through nucleic acid hybridization. Then, the siRNA-brush assembly is condensed by an ionizable and biodegradable polymer (poly(β-amino ester), PBAE) under acidic buffer condition to form a stable nanoparticle for siRNA delivery. Compared to the free siRNAs with poor complexing capability with PBAE, the large brush-like siRNA assemblies with more complicated topological architecture significantly promotes their electrostatic interaction with PBAE, enabling the formation of complexed nanoparticles at low weight ratio of polymer to siRNA. Additionally, PBAE/siRNA-brush complexes exhibit good biocompatibility and stability under physiological condition, as well as enhanced cellular internalization. When equipped with functional siRNAs, the obtained delivery system demonstrates excellent downregulation of target genes both in vitro and in vivo, through which the progression of hypertrophic scars can be retarded with negligible adverse effects in an xenografted mouse model.
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Affiliation(s)
- Xinlong Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Ding
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Guo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Jiang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yucheng Fu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lijuan Zhu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Ming Li
- Department of Dermatology, Institute of Dermatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai 200240, China
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Su CT, See DHW, Huang JW. Lipid-Based Nanocarriers in Renal RNA Therapy. Biomedicines 2022; 10:biomedicines10020283. [PMID: 35203492 PMCID: PMC8869454 DOI: 10.3390/biomedicines10020283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Kidney disease is a multifactorial problem, with a growing prevalence and an increasing global burden. With the latest worldwide data suggesting that chronic kidney disease (CKD) is the 12th leading cause of death, it is no surprise that CKD remains a public health problem that requires urgent attention. Multiple factors contribute to kidney disease, each with its own pathophysiology and pathogenesis. Furthermore, microRNAs (miRNAs) have been linked to several types of kidney diseases. As dysregulation of miRNAs is often seen in some diseases, there is potential in the exploitation of this for therapeutic applications. In addition, uptake of interference RNA has been shown to be rapid in kidneys making them a good candidate for RNA therapy. The latest advancements in RNA therapy and lipid-based nanocarriers have enhanced the effectiveness and efficiency of RNA-related drugs, thereby making RNA therapy a viable treatment option for renal disease. This is especially useful for renal diseases, for which a suitable treatment is not yet available. Moreover, the high adaptability of RNA therapy combined with the low risk of lipid-based nanocarriers make for an attractive treatment choice. Currently, there are only a small number of RNA-based drugs related to renal parenchymal disease, most of which are in different stages of clinical trials. We propose the use of miRNAs or short interfering RNAs coupled with a lipid-based nanocarrier as a delivery vehicle for managing renal disease.
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Affiliation(s)
- Chi-Ting Su
- Department of Medicine, National Taiwan University Cancer Centre, Taipei 10672, Taiwan; (C.-T.S.); (D.H.W.S.)
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Renal Division, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Douliu 640, Taiwan
| | - Daniel H. W. See
- Department of Medicine, National Taiwan University Cancer Centre, Taipei 10672, Taiwan; (C.-T.S.); (D.H.W.S.)
| | - Jenq-Wen Huang
- Renal Division, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Douliu 640, Taiwan
- Correspondence: ; Tel.: +886-5-5323911 (ext. 5675)
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