bims-limsir 2023-05-21 papers

Issue of 2023‒05‒21
five papers selected by
Ivan V. Chernikov
Institute of Сhemical Biology and Fundamental Medicine of the SB RAS

Mol Ther. 2023 May 11. pii: S1525-0016(23)00262-9. [Epub ahead of print]

Di-valent siRNA Mediated Silencing of MSH3 Blocks Somatic Repeat Expansion in Mouse Models of Huntington's Disease.

Huntington's Disease (HD) is a severe neurodegenerative disorder caused by expansion of the CAG trinucleotide repeat tract in the huntingtin gene. Inheritance of expanded CAG repeats is needed for HD manifestation, but further somatic expansion of the repeat tract in non-dividing cells, particularly striatal neurons, hastens disease onset. Called somatic repeat expansion, this process is mediated by the mismatch repair (MMR) pathway. Among MMR components identified as modifiers of HD onset, MutS Homolog 3 (MSH3) has emerged as a potentially safe and effective target for therapeutic intervention. Here, we identify fully chemically modified short interfering RNA (siRNA) that robustly silences Msh3 in vitro and in vivo. When synthesized in a di-valent scaffold, siRNA-mediated silencing of Msh3 effectively blocked CAG repeat expansion in striatum of two HD mouse models without impacting tumor-associated microsatellite instability or mRNA expression of other MMR genes. Our findings establish a promising treatment approach for patients with HD and other repeat expansion diseases.

DOI: https://doi.org/10.1016/j.ymthe.2023.05.006

Bioorg Med Chem. 2023 May 11. pii: S0968-0896(23)00165-7. [Epub ahead of print]87 117317

Synthesis and characterization of novel (S)-5'-C-aminopropyl-2'-fluorouridine modified oligonucleotides as therapeutic siRNAs.

Hitotaka Sato, Akash Chandela, Yoshihito Ueno.

The lack of stability of natural nucleosides limits their application in small interfering RNA (siRNA)-mediated RNA interference (RNAi). Various chemical modifications have been reported to improve their pharmacokinetic behavior; however, the development of potential candidates is still underway. In this study, we designed and synthesized (S)-5'-C-aminopropyl-2'-fluorouridine (5'-AP-2'-FU) and evaluated the properties of siRNAs containing this analog. A comparative thermodynamic study revealed the enhanced thermal stability of double-stranded RNAs (dsRNAs) containing 5'-AP-2'-FU in a position-specific manner, whereas (S)-5'-C-aminopropyl-2'-O-methyluridine (5'-AP-2'-MoU)-modified dsRNAs exhibited lower melting temperatures. This improved thermal stability of RNA duplexes is attributed to favorable entropy loss, which induces the duplex into an N-type (C3'-endo) conformation and enhances duplex　binding in this case. The 5'-AP-2'-FU analog was also suitable for incorporation into the passenger strand to induce gene-silencing activity. Gene knockdown efficacy was comparable to that of unmodified siRNAs, and the best response was observed by introducing 5'-AP-2'-FU near the 3'-terminal end of the passenger strand. In addition, the single-stranded RNAs (ssRNAs) modified with 5'-AP-2'-FU showed strong resistance against decomposition by nucleases when treated with buffer containing bovine serum, which was similar to 5'-AP-2'-MoU.

Keywords: Aminopropyl modification; Gene silencing; Nuclease resistance; Oligonucleotide; Thermal stability; siRNA

DOI: https://doi.org/10.1016/j.bmc.2023.117317

J Pharmacol Exp Ther. 2023 May 15. pii: JPET-MR-2023-001587. [Epub ahead of print]

Synthetic RNA therapeutics in cancer.

Youngjin Han, Seung-Hyun Shin, Chang Gyu Lim, Yong Ho Heo, In Young Choi, Ha Hyung Kim.

Recent advances in the RNA delivery system have facilitated the development of a separate field of RNA therapeutics, with modalities including mRNA, miRNA, antisense oligonucleotide (ASO), siRNA, and circular (circRNA) that have been incorporated into oncology research. The main advantages of the RNA-based modalities are high flexibility in designing RNA and rapid production for clinical screening. It is challenging to eliminate tumors by tackling a single target in cancer. In the era of precision medicine, RNA-based therapeutic approaches potentially constitute suitable platforms for targeting heterogeneous tumors that possess multiple sub-clonal cancer cell populations. In this review, we discussed how synthetic coding and non-coding RNAs, such as mRNA, miRNA, ASO, and circRNA, can be applied in the development of therapeutics. Significance Statement With development of vaccines against coronavirus, RNA-based therapeutics have received attention. Here, we discuss different types of RNA-based therapeutics potentially effective against tumor that are highly heterogeneous giving rise to resistance and relapses to the conventional therapeutics. Moreover, we summarized recent findings suggesting combination approaches of RNA therapeutics and cancer immunotherapy.

Keywords: cancer; miRNA

DOI: https://doi.org/10.1124/jpet.123.001587

Nucleic Acids Res. 2023 May 16. pii: gkad371. [Epub ahead of print]

A single-cell map of antisense oligonucleotide activity in the brain.

Meredith A Mortberg, Juliana E Gentile, Naeem M Nadaf, Charles Vanderburg, Sean Simmons, Dan Dubinsky, Adam Slamin, Salome Maldonado, Caroline L Petersen, Nichole Jones, Holly B Kordasiewicz, Hien T Zhao, Sonia M Vallabh, Eric Vallabh Minikel.

Antisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the central nervous system (CNS). By modulating RNA, they hold the promise of targeting root molecular causes of disease and hold potential to treat myriad CNS disorders. Realization of this potential requires that ASOs must be active in the disease-relevant cells, and ideally, that monitorable biomarkers also reflect ASO activity in these cells. The biodistribution and activity of such centrally delivered ASOs have been deeply characterized in rodent and non-human primate (NHP) models, but usually only in bulk tissue, limiting our understanding of the distribution of ASO activity across individual cells and across diverse CNS cell types. Moreover, in human clinical trials, target engagement is usually monitorable only in a single compartment, CSF. We sought a deeper understanding of how individual cells and cell types contribute to bulk tissue signal in the CNS, and how these are linked to CSF biomarker outcomes. We employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs against Prnp and Malat1 and NHPs treated with an ASO against PRNP. Pharmacologic activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target RNA suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction with PRNP knockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect ASO pharmacodynamic effect in disease-relevant cells in a neuronal disorder. Our results provide a reference dataset for ASO activity distribution in the CNS and establish single nucleus sequencing as a method for evaluating cell type specificity of oligonucleotide therapeutics and other modalities.

DOI: https://doi.org/10.1093/nar/gkad371

Curr Opin Toxicol. 2022 Dec;pii: 100373. [Epub ahead of print]32

Nephrotoxicity of marketed antisense oligonucleotide drugs.

Hangyu Wu, Aniket Wahane, Feryal Alhamadani, Kristy Zhang, Rajvi Parikh, SooWan Lee, Evan M McCabe, Theodore P Rasmussen, Raman Bahal, Xiao-Bo Zhong, José E Manautou.

The field of antisense oligonucleotide (ASO)-based therapies have been making strides in precision medicine due to their potent therapeutic application. Early successes in treating some genetic diseases are now attributed to an emerging class of antisense drugs. After two decades, the US Food and Drug Administration (FDA) has approved a considerable number of ASO drugs, primarily to treat rare diseases with optimal therapeutic outcomes. However, safety is one of the biggest challenges to the therapeutic utility of ASO drugs. Due to patients' and health care practitioners' urgent demands for medicines for untreatable conditions, many ASO drugs have been approved. However, a complete understanding of the mechanisms of adverse drug reactions (ADRs) and toxicities of ASOs still need to be resolved. The range of ADRs is unique to a specific drug, while few ADRs are common to a section of drugs as a whole. Nephrotoxicity is an important concern that needs to be addressed considering the clinical translation of any drug candidates ranging from small molecules to ASO-based drugs. This article encompasses what is known about the nephrotoxicity of ASO drugs, the potential mechanisms of action(s), and recommendations for future investigations on the safety of ASO drugs.

Keywords: antisense oligonucleotide drug; kidney; nephrotoxicity

DOI: https://doi.org/10.1016/j.cotox.2022.100373