1
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Alzahrani MS, Almutairy B, Althobaiti YS, Alsaab HO. Recent Advances in RNA Interference-Based Therapy for Hepatocellular Carcinoma: Emphasis on siRNA. Cell Biochem Biophys 2024:10.1007/s12013-024-01395-6. [PMID: 38987439 DOI: 10.1007/s12013-024-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2024] [Indexed: 07/12/2024]
Abstract
Even though RNA treatments were first proposed as a way to change aberrant signaling in cancer, research in this field is currently ongoing. The term "RNAi" refers to the use of several RNAi technologies, including ribozymes, riboswitches, Aptamers, small interfering RNA (siRNA), antisense oligonucleotides (ASOs), and CRISPR/Cas9 technology. The siRNA therapy has already achieved a remarkable feat by revolutionizing the treatment arena of cancers. Unlike small molecules and antibodies, which need administration every three months or even every two years, RNAi may be given every quarter to attain therapeutic results. In order to overcome complex challenges, delivering siRNAs to the targeted tissues and cells effectively and safely and improving the effectiveness of siRNAs in terms of their action, stability, specificity, and potential adverse consequences are required. In this context, the three primary techniques of siRNA therapies for hepatocellular carcinoma (HCC) are accomplished for inhibiting angiogenesis, decreasing cell proliferation, and promoting apoptosis, are discussed in this review. We also deliberate targeting issues, immunogenic reactions to siRNA therapy, and the difficulties with their intrinsic chemistry and transportation.
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Affiliation(s)
- Mohammad S Alzahrani
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif21944, Saudi Arabia
| | - Bandar Almutairy
- Department of Pharmacology, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia
| | - Yusuf S Althobaiti
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, P.O. Box 11099, Taif21944, Saudi Arabia
- Addiction and Neuroscience Research Unit, Taif University, P.O. Box 11099, Taif21944, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, P.O. Box 11099, Taif21944, Saudi Arabia.
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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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Taya T, Kami D, Teruyama F, Matoba S, Gojo S. Peptide-encoding gene transfer to modulate intracellular protein-protein interactions. Mol Ther Methods Clin Dev 2024; 32:101226. [PMID: 38516692 PMCID: PMC10952081 DOI: 10.1016/j.omtm.2024.101226] [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: 09/25/2023] [Accepted: 02/24/2024] [Indexed: 03/23/2024]
Abstract
Peptide drug discovery has great potential, but the cell membrane is a major obstacle when the target is an intracellular protein-protein interaction (PPI). It is difficult to target PPIs with small molecules; indeed, there are no intervention tools that can target any intracellular PPI. In this study, we developed a platform that enables the introduction of peptides into cells via mRNA-based gene delivery. Peptide-length nucleic acids do not enable stable ribosome binding and exhibit little to no translation into protein. In this study, a construct was created in which the sequence encoding dihydrofolate reductase (DHFR) was placed in front of the sequence encoding the target peptide, together with a translation skipping sequence, as a sequence that meets the requirements of promoting ribosome binding and rapid decay of the translated protein. This enabled efficient translation from the mRNA encoding the target protein while preventing unnecessary protein residues. Using this construct, we showed that it can inhibit Drp1/Fis1 binding, one of the intracellular PPIs, which governs mitochondrial fission, an important aspect of mitochondrial dynamics. In addition, it was shown to inhibit pathological hyperfission, normalize mitochondrial dynamics and metabolism, and inhibit apoptosis of the mitochondrial pathway.
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Affiliation(s)
- Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Fumiya Teruyama
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Pharmacology Research Department, Tokyo New Drug Research Laboratories, Kowa Company, Ltd, Tokyo, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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4
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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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5
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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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6
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Ganesh S, Kim MJ, Lee J, Feng X, Ule K, Mahan A, Krishnan HS, Wang Z, Anzahaee MY, Singhal G, Korboukh I, Lockridge JA, Sanftner L, Rijnbrand R, Abrams M, Brown BD. RNAi mediated silencing of STAT3/PD-L1 in tumor-associated immune cells induces robust anti-tumor effects in immunotherapy resistant tumors. Mol Ther 2024; 32:1895-1916. [PMID: 38549376 PMCID: PMC11184339 DOI: 10.1016/j.ymthe.2024.03.035] [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: 10/21/2023] [Revised: 01/29/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
Malignant tumors are often associated with an immunosuppressive tumor microenvironment (TME), rendering most of them resistant to standard-of-care immune checkpoint inhibitors (CPIs). Signal transducer and activator of transcription 3 (STAT3), a ubiquitously expressed transcription factor, has well-defined immunosuppressive functions in several leukocyte populations within the TME. Since the STAT3 protein has been challenging to target using conventional pharmaceutical modalities, we investigated the feasibility of applying systemically delivered RNA interference (RNAi) agents to silence its mRNA directly in tumor-associated immune cells. In preclinical rodent tumor models, chemically stabilized acylated small interfering RNAs (siRNAs) selectively silenced Stat3 mRNA in multiple relevant cell types, reduced STAT3 protein levels, and increased cytotoxic T cell infiltration. In a murine model of CPI-resistant pancreatic cancer, RNAi-mediated Stat3 silencing resulted in tumor growth inhibition, which was further enhanced in combination with CPIs. To further exemplify the utility of RNAi for cancer immunotherapy, this technology was used to silence Cd274, the gene encoding the immune checkpoint protein programmed death-ligand 1 (PD-L1). Interestingly, silencing of Cd274 was effective in tumor models that are resistant to PD-L1 antibody therapy. These data represent the first demonstration of systemic delivery of RNAi agents to the TME and suggest applying this technology for immuno-oncology applications.
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Affiliation(s)
- Shanthi Ganesh
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA.
| | - Min Ju Kim
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Jenny Lee
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Xudong Feng
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Krisjanis Ule
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Amy Mahan
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | | | - Zhe Wang
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | | | - Garima Singhal
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Ilia Korboukh
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | | | - Laura Sanftner
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Rene Rijnbrand
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Marc Abrams
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
| | - Bob D Brown
- Dicerna Pharmaceuticals, Inc, a Novo Nordisk Company, Lexington, MA 02421, USA
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7
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Salman DM, Mohammad TAM. siRNA-based therapy for gastric adenocarcinoma: what's next step? Pathol Res Pract 2024; 258:155328. [PMID: 38744002 DOI: 10.1016/j.prp.2024.155328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Gastric cancer continues to have a high death rate despite advancements in their diagnosis and treatment. Novel treatment techniques are thus desperately needed. This is where double-stranded RNA molecules known as small interfering RNA (siRNA), which may selectively target the mRNA of disease-causing genes, may find use in medicine. For siRNAs to function properly in the human body, they must be shielded from deterioration. Furthermore, in order to maintain organ function, they must only target the tumor and spare normal tissue. siRNAs have been designed using clever delivery mechanisms including polymers and lipids to achieve these objectives. Although siRNA protection is not hard to acquire, it is still challenging to target cancer cells with them. Here, we first discuss the basic characteristics of gastric cancer before describing the properties of siRNA and typical delivery methods created specifically for gastric tumors. Lastly, we provide a succinct overview of research using siRNAs to treat gastric tumors.
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Affiliation(s)
- Dyar Mudhafar Salman
- Department of Clinical Pharmacy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq; Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Talar Ahmad Merza Mohammad
- Department of Clinical Pharmacy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq; Pharmacy department, School of Medicine, University of Kurdistan Hewlêr (UKH), Erbil, Kurdistan Region, Iraq.
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8
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Sarli SL, Fakih HH, Kelly K, Devi G, Rembetsy-Brown J, McEachern H, Ferguson C, Echeverria D, Lee J, Sousa J, Sleiman H, Khvorova A, Watts J. Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo. Nucleic Acids Res 2024; 52:4799-4817. [PMID: 38613388 PMCID: PMC11109979 DOI: 10.1093/nar/gkae260] [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: 01/07/2024] [Revised: 03/06/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma multiforme is a universally lethal brain tumor that largely resists current surgical and drug interventions. Despite important advancements in understanding GBM biology, the invasiveness and heterogeneity of these tumors has made it challenging to develop effective therapies. Therapeutic oligonucleotides-antisense oligonucleotides and small-interfering RNAs-are chemically modified nucleic acids that can silence gene expression in the brain. However, activity of these oligonucleotides in brain tumors remains inadequately characterized. In this study, we developed a quantitative method to differentiate oligonucleotide-induced gene silencing in orthotopic GBM xenografts from gene silencing in normal brain tissue, and used this method to test the differential silencing activity of a chemically diverse panel of oligonucleotides. We show that oligonucleotides chemically optimized for pharmacological activity in normal brain tissue do not show consistent activity in GBM xenografts. We then survey multiple advanced oligonucleotide chemistries for their activity in GBM xenografts. Attaching lipid conjugates to oligonucleotides improves silencing in GBM cells across several different lipid classes. Highly hydrophobic lipid conjugates cholesterol and docosanoic acid enhance silencing but at the cost of higher neurotoxicity. Moderately hydrophobic, unsaturated fatty acid and amphiphilic lipid conjugates still improve activity without compromising safety. These oligonucleotide conjugates show promise for treating glioblastoma.
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Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Holly R McEachern
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - 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
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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9
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Singh D, Singh L, Kaur S, Arora A. Nucleic acids based integrated macromolecular complexes for SiRNA delivery: Recent advancements. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-24. [PMID: 38693628 DOI: 10.1080/15257770.2024.2347499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/18/2024] [Indexed: 05/03/2024]
Abstract
The therapeutic potential of small interfering RNA (siRNA) is monumental, offering a pathway to silence disease-causing genes with precision. However, the delivery of siRNA to target cells in-vivo remains a formidable challenge, owing to degradation by nucleases, poor cellular uptake and immunogenicity. This overview examines recent advancements in the design and application of nucleic acid-based integrated macromolecular complexes for the efficient delivery of siRNA. We dissect the innovative delivery vectors developed in recent years, including lipid-based nanoparticles, polymeric carriers, dendrimer complexes and hybrid systems that incorporate stimuli-responsive elements for targeted and controlled release. Advancements in bioconjugation techniques, active targeting strategies and nanotechnology-enabled delivery platforms are evaluated for their contribution to enhancing siRNA delivery. It also addresses the complex interplay between delivery system design and biological barriers, highlighting the dynamic progress and remaining hurdles in translating siRNA therapies from bench to bedside. By offering a comprehensive overview of current strategies and emerging technologies, we underscore the future directions and potential impact of siRNA delivery systems in personalized medicine.
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Affiliation(s)
- Dilpreet Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | - Lovedeep Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
| | - Simranjeet Kaur
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Akshita Arora
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
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10
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Tang Q, Khvorova A. RNAi-based drug design: considerations and future directions. Nat Rev Drug Discov 2024; 23:341-364. [PMID: 38570694 PMCID: PMC11144061 DOI: 10.1038/s41573-024-00912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
More than 25 years after its discovery, the post-transcriptional gene regulation mechanism termed RNAi is now transforming pharmaceutical development, proved by the recent FDA approval of multiple small interfering RNA (siRNA) drugs that target the liver. Synthetic siRNAs that trigger RNAi have the potential to specifically silence virtually any therapeutic target with unprecedented potency and durability. Bringing this innovative class of medicines to patients, however, has been riddled with substantial challenges, with delivery issues at the forefront. Several classes of siRNA drug are under clinical evaluation, but their utility in treating extrahepatic diseases remains limited, demanding continued innovation. In this Review, we discuss principal considerations and future directions in the design of therapeutic siRNAs, with a particular emphasis on chemistry, the application of informatics, delivery strategies and the importance of careful target selection, which together influence therapeutic success.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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11
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Chernikov IV, Bachkova IK, Sen’kova AV, Meschaninova MI, Savin IA, Vlassov VV, Zenkova MA, Chernolovskaya EL. Cholesterol-Modified Anti-Il6 siRNA Reduces the Severity of Acute Lung Injury in Mice. Cells 2024; 13:767. [PMID: 38727303 PMCID: PMC11083178 DOI: 10.3390/cells13090767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Small interfering RNA (siRNA) holds significant therapeutic potential by silencing target genes through RNA interference. Current clinical applications of siRNA have been primarily limited to liver diseases, while achievements in delivery methods are expanding their applications to various organs, including the lungs. Cholesterol-conjugated siRNA emerges as a promising delivery approach due to its low toxicity and high efficiency. This study focuses on developing a cholesterol-conjugated anti-Il6 siRNA and the evaluation of its potency for the potential treatment of inflammatory diseases using the example of acute lung injury (ALI). The biological activities of different Il6-targeted siRNAs containing chemical modifications were evaluated in J774 cells in vitro. The lead cholesterol-conjugated anti-Il6 siRNA after intranasal instillation demonstrated dose-dependent therapeutic effects in a mouse model of ALI induced by lipopolysaccharide (LPS). The treatment significantly reduced Il6 mRNA levels, inflammatory cell infiltration, and the severity of lung inflammation. IL6 silencing by cholesterol-conjugated siRNA proves to be a promising strategy for treating inflammatory diseases, with potential applications beyond the lungs.
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Affiliation(s)
- Ivan V. Chernikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Irina K. Bachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, Pirogova Str., 1, 630090 Novosibirsk, Russia
| | - Aleksandra V. Sen’kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Innokenty A. Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Valentin V. Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Marina A. Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
| | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (I.V.C.); (I.K.B.); (A.V.S.); (M.I.M.); (I.A.S.); (M.A.Z.)
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12
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Belgrad J, Fakih HH, Khvorova A. Nucleic Acid Therapeutics: Successes, Milestones, and Upcoming Innovation. Nucleic Acid Ther 2024; 34:52-72. [PMID: 38507678 DOI: 10.1089/nat.2023.0068] [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] [Indexed: 03/22/2024] Open
Abstract
Nucleic acid-based therapies have become the third major drug class after small molecules and antibodies. The role of nucleic acid-based therapies has been strengthened by recent regulatory approvals and tremendous clinical success. In this review, we look at the major obstacles that have hindered the field, the historical milestones that have been achieved, and what is yet to be resolved and anticipated soon. This review provides a view of the key innovations that are expanding nucleic acid capabilities, setting the stage for the future of nucleic acid therapeutics.
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Affiliation(s)
- Jillian Belgrad
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, 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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13
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Teng M, Xia ZJ, Lo N, Daud K, He HH. Assembling the RNA therapeutics toolbox. MEDICAL REVIEW (2021) 2024; 4:110-128. [PMID: 38680684 PMCID: PMC11046573 DOI: 10.1515/mr-2023-0062] [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: 12/01/2023] [Accepted: 02/29/2024] [Indexed: 05/01/2024]
Abstract
From the approval of COVID-19 mRNA vaccines to the 2023 Nobel Prize awarded for nucleoside base modifications, RNA therapeutics have entered the spotlight and are transforming drug development. While the term "RNA therapeutics" has been used in various contexts, this review focuses on treatments that utilize RNA as a component or target RNA for therapeutic effects. We summarize the latest advances in RNA-targeting tools and RNA-based technologies, including but not limited to mRNA, antisense oligos, siRNAs, small molecules and RNA editors. We focus on the mechanisms of current FDA-approved therapeutics but also provide a discussion on the upcoming workforces. The clinical utility of RNA-based therapeutics is enabled not only by the advances in RNA technologies but in conjunction with the significant improvements in chemical modifications and delivery platforms, which are also briefly discussed in the review. We summarize the latest RNA therapeutics based on their mechanisms and therapeutic effects, which include expressing proteins for vaccination and protein replacement therapies, degrading deleterious RNA, modulating transcription and translation efficiency, targeting noncoding RNAs, binding and modulating protein activity and editing RNA sequences and modifications. This review emphasizes the concept of an RNA therapeutic toolbox, pinpointing the readers to all the tools available for their desired research and clinical goals. As the field advances, the catalog of RNA therapeutic tools continues to grow, further allowing researchers to combine appropriate RNA technologies with suitable chemical modifications and delivery platforms to develop therapeutics tailored to their specific clinical challenges.
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Affiliation(s)
- Mona Teng
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ziting Judy Xia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nicholas Lo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Kashif Daud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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14
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Cheng SY, Caiazzi J, Biscans A, Alterman JF, Echeverria D, McHugh N, Hassler M, Jolly S, Giguere D, Cipi J, Khvorova A, Punzo C. Single intravitreal administration of a tetravalent siRNA exhibits robust and efficient gene silencing in mouse and pig photoreceptors. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102088. [PMID: 38192611 PMCID: PMC10772295 DOI: 10.1016/j.omtn.2023.102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Inherited retinal dystrophies caused by dominant mutations in photoreceptor (PR) cell expressed genes are a major cause of irreversible vision loss. Oligonucleotide therapy has been of interest in diseases that conventional medicine cannot target. In the early days, small interfering RNAs (siRNAs) were explored in clinical trials for retinal disorders with limited success due to a lack of stability and efficient cellular delivery. Thus, an unmet need exists to identify siRNA chemistry that targets PR cell expressed genes. Here, we evaluated 12 different fully chemically modified siRNA configurations, where the valency and conjugate structure were systematically altered. The impact on retinal distribution following intravitreal delivery was examined. We found that the increase in valency (tetravalent siRNA) supports the best PR accumulation. A single intravitreal administration induces multimonths efficacy in rodent and porcine retinas while demonstrating a good safety profile. The data suggest that this configuration can treat retinal diseases caused by PR cell expressed genes with 1-2 intravitreal injections per year.
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Affiliation(s)
- Shun-Yun Cheng
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurobiology, 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
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samson Jolly
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Delaney Giguere
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Joris Cipi
- Department of Ophthalmology and Visual Sciences, 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
| | - Claudio Punzo
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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15
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Tang Q, Gross KY, Fakih HH, Jackson SO, Zain U.I. Abideen M, Monopoli KR, Blanchard C, Bouix-Peter C, Portal T, Harris JE, Khvorova A, Alterman JF. Multispecies-targeting siRNAs for the modulation of JAK1 in the skin. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102117. [PMID: 38304729 PMCID: PMC10831156 DOI: 10.1016/j.omtn.2024.102117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Identifying therapeutic oligonucleotides that are cross-reactive to experimental animal species can dramatically accelerate the process of preclinical development and clinical translation. Here, we identify fully chemically-modified small interfering RNAs (siRNAs) that are cross-reactive to Janus kinase 1 (JAK1) in humans and a large variety of other species. We validated the identified siRNAs in silencing JAK1 in cell lines and skin tissues of multiple species. JAK1 is one of the four members of the JAK family of tyrosine kinases that mediate the signaling transduction of many inflammatory cytokine pathways. Dysregulation of these pathways is often involved in the pathogenesis of various immune disorders, and modulation of JAK family enzymes is an effective strategy in the clinic. Thus, this work may open up unprecedented opportunities for evaluating the modulation of JAK1 in many animal models of human inflammatory skin diseases. Further chemical engineering of the optimized JAK1 siRNAs may expand the utility of these compounds for treating immune disorders in additional tissues.
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Affiliation(s)
- Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Katherine Y. Gross
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hassan H. Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samuel O. Jackson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Kathryn R. Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | | | - John E. Harris
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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16
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La Sala L, Carlini V, Conte C, Macas-Granizo MB, Afzalpour E, Martin-Delgado J, D'Anzeo M, Pedretti RFE, Naselli A, Pontiroli AE, Cappato R. Metabolic disorders affecting the liver and heart: Therapeutic efficacy of miRNA-based therapies? Pharmacol Res 2024; 201:107083. [PMID: 38309383 DOI: 10.1016/j.phrs.2024.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
Liver and heart disease are major causes of death worldwide. It is known that metabolic alteration causing type 2 diabetes (T2D) and Nonalcoholic fatty liver (NAFLD) coupled with a derangement in lipid homeostasis, may exacerbate hepatic and cardiovascular diseases. Some pharmacological treatments can mitigate organ dysfunctions but the important side effects limit their efficacy leading often to deterioration of the tissues. It needs to develop new personalized treatment approaches and recent progresses of engineered RNA molecules are becoming increasingly viable as alternative treatments. This review outlines the current use of antisense oligonucleotides (ASOs), RNA interference (RNAi) and RNA genome editing as treatment for rare metabolic disorders. However, the potential for small non-coding RNAs to serve as therapeutic agents for liver and heart diseases is yet to be fully explored. Although miRNAs are recognized as biomarkers for many diseases, they are also capable of serving as drugs for medical intervention; several clinical trials are testing miRNAs as therapeutics for type 2 diabetes, nonalcoholic fatty liver as well as cardiac diseases. Recent advances in RNA-based therapeutics may potentially facilitate a novel application of miRNAs as agents and as druggable targets. In this work, we sought to summarize the advancement and advantages of miRNA selective therapy when compared to conventional drugs. In particular, we sought to emphasise druggable miRNAs, over ASOs or other RNA therapeutics or conventional drugs. Finally, we sought to address research questions related to efficacy, side-effects, and range of use of RNA therapeutics. Additionally, we covered hurdles and examined recent advances in the use of miRNA-based RNA therapy in metabolic disorders such as diabetes, liver, and heart diseases.
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Affiliation(s)
- Lucia La Sala
- IRCCS MultiMedica, 20138 Milan, Italy; Dept. of Biomedical Sciences for Health, University of Milan, Milan, Italy.
| | | | - Caterina Conte
- IRCCS MultiMedica, 20138 Milan, Italy; Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy
| | | | - Elham Afzalpour
- Dept. of Biomedical Sciences and Clinic, University of Milan, Milan, Italy
| | - Jimmy Martin-Delgado
- Hospital Luis Vernaza, Junta de Beneficiencia de Guayaquil, 090603 Guayaquil, Ecuador; Instituto de Investigacion e Innovacion en Salud Integral, Universidad Catolica de Santiago de Guayaquil, Guayaquil 090603, Ecuador
| | - Marco D'Anzeo
- AUO delle Marche, SOD Medicina di Laboratorio, Ancona, Italy
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17
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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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18
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Chernikov IV, Ponomareva UA, Meschaninova MI, Bachkova IK, Vlassov VV, Zenkova MA, Chernolovskaya EL. Cholesterol Conjugates of Small Interfering RNA: Linkers and Patterns of Modification. Molecules 2024; 29:786. [PMID: 38398538 PMCID: PMC10892548 DOI: 10.3390/molecules29040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Cholesterol siRNA conjugates attract attention because they allow the delivery of siRNA into cells without the use of transfection agents. In this study, we compared the efficacy and duration of silencing induced by cholesterol conjugates of selectively and totally modified siRNAs and their heteroduplexes of the same sequence and explored the impact of linker length between the 3' end of the sense strand of siRNA and cholesterol on the silencing activity of "light" and "heavy" modified siRNAs. All 3'-cholesterol conjugates were equally active under transfection, but the conjugate with a C3 linker was less active than those with longer linkers (C8 and C15) in a carrier-free mode. At the same time, they were significantly inferior in activity to the 5'-cholesterol conjugate. Shortening the sense strand carrying cholesterol by two nucleotides from the 3'-end did not have a significant effect on the activity of the conjugate. Replacing the antisense strand or both strands with fully modified ones had a significant effect on silencing as well as improving the duration in transfection-mediated and carrier-free modes. A significant 78% suppression of MDR1 gene expression in KB-8-5 xenograft tumors developed in mice promises an advantage from the use of fully modified siRNA cholesterol conjugates in combination chemotherapy.
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Affiliation(s)
- Ivan V Chernikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Ul'yana A Ponomareva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Mariya I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Irina K Bachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Pirogova Str. 1, 630090 Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Academic Lavrentiev Avenue 8, 630090 Novosibirsk, Russia
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19
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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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20
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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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21
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Zharkov TD, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Influence of Combinations of Lipophilic and Phosphate Backbone Modifications on Cellular Uptake of Modified Oligonucleotides. Molecules 2024; 29:452. [PMID: 38257365 PMCID: PMC10818405 DOI: 10.3390/molecules29020452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous types of oligonucleotide modifications have been developed since automated synthesis of DNA/RNA became a common instrument in the creation of synthetic oligonucleotides. Despite the growing number of types of oligonucleotide modifications under development, only a few of them and, moreover, their combinations have been studied widely enough in terms of their influence on the properties of corresponding NA constructions. In the present study, a number of oligonucleotides with combinations of 3'-end lipophilic (a single cholesteryl or a pair of dodecyl residues) and phosphate backbone modifications were synthesized. The influence of the combination of used lipophilic groups with phosphate modifications of various natures and different positions on the efficiency of cell penetration was evaluated. The obtained results indicate that even a couple of phosphate modifications are able to affect a set of oligonucleotide properties in a complex manner and can remarkably change cellular uptake. These data clearly show that the strategy of using different patterns of modification combinations has great potential for the rational design of oligonucleotide structures with desired predefined properties.
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Affiliation(s)
| | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (O.V.M.); (S.A.Z.); (S.N.K.)
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22
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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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23
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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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24
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Guo S, Zhang M, Huang Y. Three 'E' challenges for siRNA drug development. Trends Mol Med 2024; 30:13-24. [PMID: 37951790 DOI: 10.1016/j.molmed.2023.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
siRNA therapeutics have gained extensive attention, and to date six siRNAs are approved for clinical use. Despite being investigated for the treatment of metabolic, cardiovascular, infectious, and rare genetic diseases, cancer, and central nervous system (CNS) disorders, there exist several druggability challenges. Here, we provide insightful discussions concerning these challenges, comprising targeted accumulation and cellular uptake ('entry'), endolysosomal escape ('escape'), and in vivo pharmaceutical performance ('efficacy') - the three 'E' challenges - while also shedding light on siRNA drug development. Moreover, we propose several promising strategies that hold great potential in facilitating the clinical translation of siRNA therapeutics, including the exploration of diverse ligand-siRNA conjugates, expansion of potential disease targets, and excavation of novel modification geometries, as well as the development of combination therapies.
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Affiliation(s)
- Shuai Guo
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China
| | - Mengjie Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China
| | - Yuanyu Huang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing 100081, China; Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China; Rigerna Therapeutics, Suzhou, Jiangsu 215127, China; Rigerna Therapeutics, Beijing 102629, China.
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25
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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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26
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Bauer I, Ilina E, Zharkov T, Grigorieva E, Chinak O, Kupryushkin M, Golyshev V, Mitin D, Chubarov A, Khodyreva S, Dmitrienko E. Self-Penetrating Oligonucleotide Derivatives: Features of Self-Assembly and Interactions with Serum and Intracellular Proteins. Pharmaceutics 2023; 15:2779. [PMID: 38140119 PMCID: PMC10747088 DOI: 10.3390/pharmaceutics15122779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Lipophilic oligonucleotide derivatives are a potent approach to the intracellular delivery of nucleic acids. The binding of these derivatives to serum albumin is a determinant of their fate in the body, as its structure contains several sites of high affinity for hydrophobic compounds. This study focuses on the features of self-association and non-covalent interactions with human serum albumin of novel self-penetrating oligonucleotide derivatives. The study revealed that the introduction of a triazinyl phosphoramidate modification bearing two dodecyl groups at the 3' end region of the oligonucleotide sequence has a negligible effect on its affinity for the complementary sequence. Dynamic light scattering verified that the amphiphilic oligonucleotides under study can self-assemble into micelle-like particles ranging from 8 to 15 nm in size. The oligonucleotides with dodecyl groups form stable complexes with human serum albumin with a dissociation constant of approximately 10-6 M. The oligonucleotide micelles are simultaneously destroyed upon binding to albumin. Using an electrophoretic mobility shift assay and affinity modification, we examined the ability of DNA duplexes containing triazinyl phosphoramidate oligonucleotides to interact with Ku antigen and PARP1, as well as the mutual influence of PARP1 and albumin or Ku antigen and albumin upon interaction with DNA duplexes. These findings, together with the capability of dodecyl-containing derivatives to effectively penetrate different cells, such as HEK293 and T98G, indicate that the oligonucleotides under study can be considered as a platform for the development of therapeutic preparations with a target effect.
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Affiliation(s)
- Irina Bauer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ekaterina Ilina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Timofey Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Evgeniya Grigorieva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Olga Chinak
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Maxim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Victor Golyshev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Dmitry Mitin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Svetlana Khodyreva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Elena Dmitrienko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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27
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Fakih HH, Tang Q, Summers A, Shin M, Buchwald JE, Gagnon R, Hariharan VN, Echeverria D, Cooper DA, Watts JK, Khvorova A, Sleiman HF. Dendritic amphiphilic siRNA: Selective albumin binding, in vivo efficacy, and low toxicity. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102080. [PMID: 38089931 PMCID: PMC10711485 DOI: 10.1016/j.omtn.2023.102080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/14/2023] [Indexed: 01/12/2024]
Abstract
Although an increasing number of small interfering RNA (siRNA) therapies are reaching the market, the challenge of efficient extra-hepatic delivery continues to limit their full therapeutic potential. Drug delivery vehicles and hydrophobic conjugates are being used to overcome the delivery bottleneck. Previously, we reported a novel dendritic conjugate that can be appended efficiently to oligonucleotides, allowing them to bind albumin with nanomolar affinity. Here, we explore the ability of this novel albumin-binding conjugate to improve the delivery of siRNA in vivo. We demonstrate that the conjugate binds albumin exclusively in circulation and extravasates to various organs, enabling effective gene silencing. Notably, we show that the conjugate achieves a balance between hydrophobicity and safety, as it significantly reduces the side effects associated with siRNA interactions with blood components, which are commonly observed in some hydrophobically conjugated siRNAs. In addition, it reduces siRNA monocyte uptake, which may lead to cytokine/inflammatory responses. This work showcases the potential of using this dendritic conjugate as a selective albumin binding handle for the effective and safe delivery of nucleic acid therapeutics. We envision that these properties may pave the way for new opportunities to overcome delivery hurdles of oligonucleotides in future applications.
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Affiliation(s)
- Hassan H. Fakih
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- 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
| | - Ashley Summers
- 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
- College of Pharmacy, Sookmyung Women’s University, Yongsan-gu, Seoul, Korea
| | - Julianna E. Buchwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rosemary Gagnon
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Vignesh N. Hariharan
- 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 A. Cooper
- RNA Therapeutics Institute, 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
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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28
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Tang Q, Fakih HH, Zain Ui Abideen M, Hildebrand SR, Afshari K, Gross KY, Sousa J, Maebius AS, Bartholdy C, Søgaard PP, Jackerott M, Hariharan V, Summers A, Fan X, Okamura K, Monopoli KR, Cooper DA, Echeverria D, Bramato B, McHugh N, Furgal RC, Dresser K, Winter SJ, Biscans A, Chuprin J, Haddadi NS, Sherman S, Yıldız-Altay Ü, Rashighi M, Richmond JM, Bouix-Peter C, Blanchard C, Clauss A, Alterman JF, Khvorova A, Harris JE. Rational design of a JAK1-selective siRNA inhibitor for the modulation of autoimmunity in the skin. Nat Commun 2023; 14:7099. [PMID: 37925520 PMCID: PMC10625637 DOI: 10.1038/s41467-023-42714-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Inhibition of Janus kinase (JAK) family enzymes is a popular strategy for treating inflammatory and autoimmune skin diseases. In the clinic, small molecule JAK inhibitors show distinct efficacy and safety profiles, likely reflecting variable selectivity for JAK subtypes. Absolute JAK subtype selectivity has not yet been achieved. Here, we rationally design small interfering RNAs (siRNAs) that offer sequence-specific gene silencing of JAK1, narrowing the spectrum of action on JAK-dependent cytokine signaling to maintain efficacy and improve safety. Our fully chemically modified siRNA supports efficient silencing of JAK1 expression in human skin explant and modulation of JAK1-dependent inflammatory signaling. A single injection into mouse skin enables five weeks of duration of effect. In a mouse model of vitiligo, local administration of the JAK1 siRNA significantly reduces skin infiltration of autoreactive CD8+ T cells and prevents epidermal depigmentation. This work establishes a path toward siRNA treatments as a new class of therapeutic modality for inflammatory and autoimmune skin diseases.
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Affiliation(s)
- Qi Tang
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Mohammad Zain Ui Abideen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Samuel R Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Khashayar Afshari
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Katherine Y Gross
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Allison S Maebius
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | | | | | - Vignesh Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Xueli Fan
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ken Okamura
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kathryn R Monopoli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - David A Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Raymond C Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karen Dresser
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Sarah J Winter
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jane Chuprin
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nazgol-Sadat Haddadi
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Shany Sherman
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Ümmügülsüm Yıldız-Altay
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Mehdi Rashighi
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jillian M Richmond
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | | | - Adam Clauss
- LEO Pharma A/S, Industriparken 55, 2750, Ballerup, Denmark
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| | - John E Harris
- Department of Dermatology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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29
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Sparmann A, Vogel J. RNA-based medicine: from molecular mechanisms to therapy. EMBO J 2023; 42:e114760. [PMID: 37728251 PMCID: PMC10620767 DOI: 10.15252/embj.2023114760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
RNA-based therapeutics have the potential to revolutionize the treatment and prevention of human diseases. While early research faced setbacks, it established the basis for breakthroughs in RNA-based drug design that culminated in the extraordinarily fast development of mRNA vaccines to combat the COVID-19 pandemic. We have now reached a pivotal moment where RNA medicines are poised to make a broad impact in the clinic. In this review, we present an overview of different RNA-based strategies to generate novel therapeutics, including antisense and RNAi-based mechanisms, mRNA-based approaches, and CRISPR-Cas-mediated genome editing. Using three rare genetic diseases as examples, we highlight the opportunities, but also the challenges to wide-ranging applications of this class of drugs.
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Affiliation(s)
- Anke Sparmann
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
| | - Jörg Vogel
- Helmholtz Institute for RNA‐based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI)WürzburgGermany
- Institute of Molecular Infection Biology (IMIB)University of WürzburgWürzburgGermany
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30
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Ranasinghe P, Addison ML, Dear JW, Webb DJ. Small interfering RNA: Discovery, pharmacology and clinical development-An introductory review. Br J Pharmacol 2023; 180:2697-2720. [PMID: 36250252 DOI: 10.1111/bph.15972] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/28/2022] Open
Abstract
Post-transcriptional gene silencing targets and degrades mRNA transcripts, silencing the expression of specific genes. RNA interference technology, using synthetic structurally well-defined short double-stranded RNA (small interfering RNA [siRNA]), has advanced rapidly in recent years. This introductory review describes the utility of siRNA, by exploring the underpinning biology, pharmacology, recent advances and clinical developments, alongside potential limitations and ongoing challenges. Mediated by the RNA-induced silencing complex, siRNAs bind to specific complementary mRNAs, which are subsequently degraded. siRNA therapy offers advantages over other therapeutic approaches, including ability of specifically designed siRNAs to potentially target any mRNA and improved patient adherence through infrequent administration associated with a very long duration of action. Key pharmacokinetic and pharmacodynamic challenges include targeted administration, poor tissue penetration, nuclease inactivation, rapid renal elimination, immune activation and off-target effects. These have been overcome by chemical modification of siRNA and/or by utilising a range of delivery systems, increasing bioavailability and stability to allow successful clinical translation. Patisiran (hereditary transthyretin-mediated amyloidosis) was the first licensed siRNA, followed by givosiran (acute hepatic porphyria), lumasiran (primary hyperoxaluria type 1) and inclisiran (familial hypercholesterolaemia), which all use N-acetylgalactosamine (GalNAc) linkage for effective liver-directed delivery. Others are currently under development for indications varying from rare genetic diseases to common chronic non-communicable diseases (hypertension, cancer). Technological advances are paving the way for broader clinical use. Ongoing challenges remain in targeting organs beyond the liver and reaching special sites (e.g., brain). By overcoming these barriers, siRNA therapy has the potential to substantially widen its therapeutic impact.
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Affiliation(s)
- Priyanga Ranasinghe
- Department of Pharmacology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Melisande L Addison
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - James W Dear
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - David J Webb
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
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31
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Lee JW, Choi J, Kim EH, Choi J, Kim SH, Yang Y. Design of siRNA Bioconjugates for Efficient Control of Cancer-Associated Membrane Receptors. ACS OMEGA 2023; 8:36435-36448. [PMID: 37810687 PMCID: PMC10552107 DOI: 10.1021/acsomega.3c05395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Research on siRNA delivery has seen tremendous growth over the past few decades. As one of the major delivery strategies, siRNA bioconjugates offer the potential to enhance and extend the pharmacological properties of siRNAs while minimizing toxicity. In this paper, we suggest the development of a siRNA conjugate platform with peptides and proteins that are ligands of target receptors for cancer treatment. The siRNA bioconjugates target and block the receptor membrane proteins, enter the cells through receptor-mediated endocytosis, and inhibit the expression of that same target membrane receptor, thereby doubly controlling the function of the membrane proteins. The three kinds of bioconjugates targeting CD47, PD-L1, and EGFR were synthesized via two different copper-free click chemistry reactions. Results showed the cellular uptake of each conjugate, reduction of target gene expression, and efficient functional control of receptor proteins. This platform provides an effective approach for regulating membrane proteins in various diseases beyond cancer.
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Affiliation(s)
- Jong Won Lee
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jiwoong Choi
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Eun Hye Kim
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department
of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jiwon Choi
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department
of Bioengineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sun Hwa Kim
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Yoosoo Yang
- Medicinal
Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
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32
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Zharkov TD, Mironova EM, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Fork- and Comb-like Lipophilic Structures: Different Chemical Approaches to the Synthesis of Oligonucleotides with Multiple Dodecyl Residues. Int J Mol Sci 2023; 24:14637. [PMID: 37834092 PMCID: PMC10572690 DOI: 10.3390/ijms241914637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like dodecyl-containing oligonucleotide structures were performed, including use of non-nucleotide units and different types of phosphate modifications such as alkyl phosphoramidate, phosphoryl guanidine, and triazinyl phosphoramidate. The influence of the number of introduced lipophilic residues, their mutual arrangement, and the type of formed modification backbone on cell penetration was evaluated. The results obtained indicate great potential in the developed chemical approaches, not only for the synthesis of complex oligonucleotide structures but also for the fine-tuning of their properties.
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Affiliation(s)
| | | | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (E.M.M.); (O.V.M.); (S.A.Z.); (S.N.K.)
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33
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Cheng SY, Caiazzi J, Biscans A, Alterman JF, Echeverria D, McHugh N, Hassler M, Jolly S, Giguere D, Cipi J, Khvorova A, Punzo C. Single intravitreal administration of a tetravalent siRNA exhibits robust and efficient gene silencing in rodent and swine photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558641. [PMID: 37790464 PMCID: PMC10542117 DOI: 10.1101/2023.09.20.558641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Inherited retinal dystrophies caused by dominant mutations in photoreceptor-expressed genes, are a major cause of irreversible vision loss. Oligonucleotide therapy has been of interest in diseases that conventional medicine cannot target. In the early days, small interfering RNAs (siRNAs) were explored in clinical trials for retinal disorders with limited success due to a lack of stability and efficient cellular delivery. Thus, an unmet need exists to identify siRNA chemistry that targets photoreceptor-expressed genes. Here we evaluated 12 different fully chemically modified siRNA configurations, where the valency and conjugate structure were systematically altered. The impact on retinal distribution following intravitreal delivery was examined. We found that the increase in valency (tetravalent siRNA) supports the best photoreceptor accumulation. A single intravitreal administration induces multi-months efficacy in rodent and porcine retinas while showing a good safety profile. The data suggest that this configuration can treat retinal diseases caused by photoreceptor-expressed genes with 1-2 intravitreal injections per year.
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34
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Brentari I, Zadorozhna M, Denti MA, Giorgio E. RNA therapeutics for neurological diseases. Br Med Bull 2023; 147:50-61. [PMID: 37210633 DOI: 10.1093/bmb/ldad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023]
Abstract
INTRODUCTION Ribonucleic acid (RNA) therapeutics are a new class of drugs whose importance is highlighted by the growing number of molecules in the clinic. SOURCES OF DATA We focus on RNA therapeutics for neurogenetic disorders, which are broadly defined as diseases with a genetic background and with at least one clinical sign affecting the nervous system. A systematic search identified 14 RNA drugs approved by FDA and many others in development. AREAS OF AGREEMENT The field of RNA therapeutics is changing the therapeutic scenario across many disorders. AREAS OF CONTROVERSY Despite its recent successes, RNA therapeutics encountered several hurdles and some clinical failures. Delivery to the brain represents the biggest challenge. GROWING POINTS The many advantages of RNA drugs make the development of these technologies a worthwhile investment. AREAS TIMELY FOR DEVELOPING RESEARCH Clinical failures stress the importance of implementing clinical trial design and optimizing RNA molecules to hold the promise of revolutionizing the treatment of human diseases.
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Affiliation(s)
- Ilaria Brentari
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università degli Studi di Trento, 38123 Trento, Italy
| | - Mariia Zadorozhna
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Michela Alessandra Denti
- Dipartimento di Biologia Cellulare, Computazionale e Integrata (CIBIO), Università degli Studi di Trento, 38123 Trento, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
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35
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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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36
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Philippou S, Mastroyiannopoulos NP, Tomazou M, Oulas A, Ackers-Johnson M, Foo RS, Spyrou GM, Phylactou LA. Selective Delivery to Cardiac Muscle Cells Using Cell-Specific Aptamers. Pharmaceuticals (Basel) 2023; 16:1264. [PMID: 37765072 PMCID: PMC10534653 DOI: 10.3390/ph16091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
In vivo SELEX is an advanced adaptation of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) that allows the development of aptamers capable of recognizing targets directly within their natural microenvironment. While this methodology ensures a higher translation potential for the selected aptamer, it does not select for aptamers that recognize specific cell types within a tissue. Such aptamers could potentially improve the development of drugs for several diseases, including neuromuscular disorders, by targeting solely the proteins involved in their pathogenesis. Here, we describe our attempt to utilize in vivo SELEX with a modification in the methodology that drives the selection of intravenously injected aptamers towards a specific cell type of interest. Our data suggest that the incorporation of a cell enrichment step can direct the in vivo localization of RNA aptamers into cardiomyocytes, the cardiac muscle cells, more readily over other cardiac cells. Given the crucial role of cardiomyocytes in the disease pathology in DMD cardiomyopathy and therapy, these aptamers hold great potential as drug delivery vehicles with cardiomyocyte selectivity.
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Affiliation(s)
- Styliana Philippou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Nikolaos P. Mastroyiannopoulos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Marios Tomazou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Anastasios Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Matthew Ackers-Johnson
- Cardiovascular Research Institute, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Roger S. Foo
- Cardiovascular Research Institute, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore
| | - George M. Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
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37
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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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38
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Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. RESEARCH SQUARE 2023:rs.3.rs-2987323. [PMID: 37398145 PMCID: PMC10312934 DOI: 10.21203/rs.3.rs-2987323/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~ 32-fold over PS backbone and > 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~ 6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
| | | | | | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Qi Tang
- University of Massachusetts Chan Medical School
| | | | | | | | | | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Bruno Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | | | - Neil Aronin
- University of Massachusetts Worcester Campus
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39
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BM, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542506. [PMID: 37292886 PMCID: PMC10245983 DOI: 10.1101/2023.05.26.542506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Vignesh Narayan Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Chantal Furguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Hassan Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Qi Tan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Raymond C. Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew R. Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
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40
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Thomaidou AC, Goulielmaki M, Tsintarakis A, Zoumpourlis P, Toya M, Christodoulou I, Zoumpourlis V. miRNA-Guided Regulation of Mesenchymal Stem Cells Derived from the Umbilical Cord: Paving the Way for Stem-Cell Based Regeneration and Therapy. Int J Mol Sci 2023; 24:ijms24119189. [PMID: 37298143 DOI: 10.3390/ijms24119189] [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] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
The human body is an abundant source of multipotent cells primed with unique properties that can be exploited in a multitude of applications and interventions. Mesenchymal stem cells (MSCs) represent a heterogenous population of undifferentiated cells programmed to self-renew and, depending on their origin, differentiate into distinct lineages. Alongside their proven ability to transmigrate toward inflammation sites, the secretion of various factors that participate in tissue regeneration and their immunoregulatory function render MSCs attractive candidates for use in the cytotherapy of a wide spectrum of diseases and conditions, as well as in different aspects of regenerative medicine. In particular, MSCs that can be found in fetal, perinatal, or neonatal tissues possess additional capabilities, including predominant proliferation potential, increased responsiveness to environmental stimuli, and hypoimmunogenicity. Since microRNA (miRNA)-guided gene regulation governs multiple cellular functions, miRNAs are increasingly being studied in the context of driving the differentiation process of MSCs. In the present review, we explore the mechanisms of miRNA-directed differentiation of MSCs, with a special focus on umbilical cord-derived mesenchymal stem cells (UCMSCs), and we identify the most relevant miRNAs and miRNA sets and signatures. Overall, we discuss the potent exploitations of miRNA-driven multi-lineage differentiation and regulation of UCMSCs in regenerative and therapeutic protocols against a range of diseases and/or injuries that will achieve a meaningful clinical impact through maximizing treatment success rates, while lacking severe adverse events.
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Affiliation(s)
- Arsinoe C Thomaidou
- Laboratory of Clinical Virology, Medical School, University of Crete, 71500 Heraklion, Greece
| | - Maria Goulielmaki
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece
| | - Antonis Tsintarakis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Panagiotis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Marialena Toya
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Ioannis Christodoulou
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece
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41
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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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42
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Kodr D, Kužmová E, Pohl R, Kraus T, Hocek M. Lipid-linked nucleoside triphosphates for enzymatic synthesis of hydrophobic oligonucleotides with enhanced membrane anchoring efficiency. Chem Sci 2023; 14:4059-4069. [PMID: 37063801 PMCID: PMC10094435 DOI: 10.1039/d2sc06718h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/19/2023] [Indexed: 03/22/2023] Open
Abstract
We designed and synthesized a series of 2'-deoxyribonucleoside triphosphates (dNTPs) bearing various lipid moieties. Fatty acid- and cholesterol-modified dNTPs proved to be substrates for KOD XL DNA polymerase in primer extension reactions. They were also mutually compatible for simultaneous multiple incorporations into the DNA strand. The methodology of enzymatic synthesis opened a pathway to diverse structurally unique lipid-ON probes containing one or more lipid units. We studied interactions of such probes with the plasma membranes of live cells. Employing a rational design, we found a series of lipid-ONs with enhanced membrane anchoring efficiency. The in-membrane stability of multiply modified ONs was superior to that of commonly studied ON analogues, in which a single cholesterol molecule is typically tethered to the thread end. Notably, some of the probes were detected at the cell surface even after 24 h upon removal of the probe solution. Such an effect was general to several studied cell lines.
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Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague Hlavova 8 Prague-2 12843 Czech Republic
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43
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Dowdy SF. Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem? RNA (NEW YORK, N.Y.) 2023; 29:396-401. [PMID: 36669888 PMCID: PMC10019367 DOI: 10.1261/rna.079507.122] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/09/2023] [Indexed: 05/15/2023]
Abstract
With over 15 FDA approved drugs on the market and numerous ongoing clinical trials, RNA therapeutics, such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs), have shown great potential to treat human disease. Their mechanism of action is based entirely on the sequence of validated disease-causing genes without the prerequisite knowledge of protein structure, activity or cellular location. In contrast to small molecule therapeutics that passively diffuse across the cell membrane's lipid bilayer, RNA therapeutics are too large, too charged, and/or too hydrophilic to passively diffuse across the cellular membrane and instead are taken up into cells by endocytosis. However, endosomes are also composed of a lipid bilayer barrier that results in endosomal capture and retention of 99% of RNA therapeutics with 1% or less entering the cytoplasm. Although this very low level of endosomal escape has proven sufficient for liver and some CNS disorders, it is insufficient for the vast majority of extra-hepatic diseases. Unfortunately, there are currently no acceptable solutions to the endosomal escape problem. Consequently, before RNA therapeutics can be used to treat widespread human disease, the rate-limiting delivery problem of endosomal escape must be solved in a nontoxic manner.
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Affiliation(s)
- Steven F Dowdy
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, USA
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44
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Hall J. Future directions for medicinal chemistry in the field of oligonucleotide therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:423-433. [PMID: 36693762 PMCID: PMC10019366 DOI: 10.1261/rna.079511.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 05/13/2023]
Abstract
In the last decade, the field of oligonucleotide therapeutics has matured, with the regulatory approval of several single-stranded and double-stranded RNA drugs. In this Perspective, I discuss enabling developments and likely future directions in the field from the perspective of oligonucleotide chemistry.
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Affiliation(s)
- Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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45
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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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46
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Sell MC, Ramlogan-Steel CA, Steel JC, Dhungel BP. MicroRNAs in cancer metastasis: biological and therapeutic implications. Expert Rev Mol Med 2023; 25:e14. [PMID: 36927814 PMCID: PMC10407223 DOI: 10.1017/erm.2023.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/02/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Cancer metastasis is the primary cause of cancer-related deaths. The seeding of primary tumours at a secondary site is a highly inefficient process requiring substantial alterations in the genetic architecture of cancer cells. These alterations include significant changes in global gene expression patterns. MicroRNAs are small, non-protein coding RNAs which play a central role in regulating gene expression. Here, we focus on microRNA determinants of cancer metastasis and examine microRNA dysregulation in metastatic cancer cells. We dissect the metastatic process in a step-wise manner and summarise the involvement of microRNAs at each step. We also discuss the advantages and limitations of different microRNA-based strategies that have been used to target metastasis in pre-clinical models. Finally, we highlight current clinical trials that use microRNA-based therapies to target advanced or metastatic tumours.
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Affiliation(s)
- Marie C. Sell
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Charmaine A. Ramlogan-Steel
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Jason C. Steel
- School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, QLD 4701, Australia
| | - Bijay P. Dhungel
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Camperdown, NSW 2050, Australia
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47
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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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48
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MicroRNA as a Diagnostic Tool, Therapeutic Target and Potential Biomarker in Cutaneous Malignant Melanoma Detection—Narrative Review. Int J Mol Sci 2023; 24:ijms24065386. [PMID: 36982460 PMCID: PMC10048937 DOI: 10.3390/ijms24065386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Melanoma is the most serious type of skin cancer, causing a large majority of deaths but accounting for only ~1% of all skin cancer cases. The worldwide incidence of malignant melanoma is increasing, causing a serious socio-economic problem. Melanoma is diagnosed mainly in young and middle-aged people, which distinguishes it from other solid tumors detected mainly in mature people. The early detection of cutaneous malignant melanoma (CMM) remains a priority and it is a key factor limiting mortality. Doctors and scientists around the world want to improve the quality of diagnosis and treatment, and are constantly looking for new, promising opportunities, including the use of microRNAs (miRNAs), to fight melanoma cancer. This article reviews miRNA as a potential biomarker and diagnostics tool as a therapeutic drugs in CMM treatment. We also present a review of the current clinical trials being carried out worldwide, in which miRNAs are a target for melanoma treatment.
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49
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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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50
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Tanaka Y, Tanioku Y, Nakayama T, Aso K, Yamaguchi T, Kamada H, Obika S. Synthesis of multivalent fatty acid-conjugated antisense oligonucleotides: Cell internalization, physical properties, and in vitro and in vivo activities. Bioorg Med Chem 2023; 81:117192. [PMID: 36780806 DOI: 10.1016/j.bmc.2023.117192] [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] [Received: 12/23/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Herein, we describe the design and synthesis of multi-conjugatable fatty acid monomer phosphoramidites and their conjugation to antisense oligonucleotides (ASOs). Multivalent long-chain fatty acid conjugation improved the cellular uptake of ASOs but decreased in vitro activity due to alterations in physical properties and cellular localization. In addition, multivalently fatty acid-conjugated ASOs showed different organ specificity compared with that of unconjugated ASO in in vivo experiment. Although optimization of the linker structure between the fatty acid moiety and the ASO may be required, divalent long-chain fatty acid conjugation provides a new approach to increase endocytosis, thereby potentially improving the activity of therapeutic ASOs.
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Affiliation(s)
- Yuya Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yurika Tanioku
- School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taisuke Nakayama
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kotomi Aso
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Haruhiko Kamada
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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