1
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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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2
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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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3
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Miller R, Paquette J, Barker A, Sapp E, McHugh N, Bramato B, Yamada N, Alterman J, Echeveria D, Yamada K, Watts J, Anaclet C, DiFiglia M, Khvorova A, Aronin N. Preventing acute neurotoxicity of CNS therapeutic oligonucleotides with the addition of Ca 2+ and Mg 2+ in the formulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597639. [PMID: 38895198 PMCID: PMC11185713 DOI: 10.1101/2024.06.06.597639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Oligonucleotide therapeutics (ASOs and siRNAs) have been explored for modulation of gene expression in the central nervous system (CNS), with several drugs approved and many in clinical evaluation. Administration of highly concentrated oligonucleotides to the CNS can induce acute neurotoxicity. We demonstrate that delivery of concentrated oligonucleotides to the CSF in awake mice induces acute toxicity, observable within seconds of injection. Electroencephalography (EEG) and electromyography (EMG) in awake mice demonstrated seizures. Using ion chromatography, we show that siRNAs can tightly bind Ca2+ and Mg2+ up to molar equivalents of the phosphodiester (PO)/phosphorothioate (PS) bonds independently of the structure or phosphorothioate content. Optimization of the formulation by adding high concentrations (above biological levels) of divalent cations (Ca2+ alone, Mg2+ alone, or Ca2+ and Mg2+) prevents seizures with no impact on the distribution or efficacy of the oligonucleotide. The data here establishes the importance of adding Ca2+ and Mg2+ to the formulation for the safety of CNS administration of therapeutic oligonucleotides.
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Affiliation(s)
- Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
- Department of Medicine, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
- Department of Medicine, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Alexandra Barker
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
- Department of Medicine, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Ellen Sapp
- MassGeneral Institute for Neurodegenerative Disease, 114 16 Street, Charlestown MA, 02129
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Julia Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Dimas Echeveria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Jonathan Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Christelle Anaclet
- Department of Neurologic Surgery, University of California Davis School of Medicine, Davis, CA, 95618
| | - Marian DiFiglia
- MassGeneral Institute for Neurodegenerative Disease, 114 16 Street, Charlestown MA, 02129
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
- Department of Medicine, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA, 01605
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4
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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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5
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Han B, Liang W, Li XJ, Li S, Yan S, Tu Z. Large animal models for Huntington's disease research. Zool Res 2024; 45:275-283. [PMID: 38485497 PMCID: PMC11017086 DOI: 10.24272/j.issn.2095-8137.2023.199] [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: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 03/19/2024] Open
Abstract
Huntington's disease (HD) is a hereditary neurodegenerative disorder for which there is currently no effective treatment available. Consequently, the development of appropriate disease models is critical to thoroughly investigate disease progression. The genetic basis of HD involves the abnormal expansion of CAG repeats in the huntingtin ( HTT) gene, leading to the expansion of a polyglutamine repeat in the HTT protein. Mutant HTT carrying the expanded polyglutamine repeat undergoes misfolding and forms aggregates in the brain, which precipitate selective neuronal loss in specific brain regions. Animal models play an important role in elucidating the pathogenesis of neurodegenerative disorders such as HD and in identifying potential therapeutic targets. Due to the marked species differences between rodents and larger animals, substantial efforts have been directed toward establishing large animal models for HD research. These models are pivotal for advancing the discovery of novel therapeutic targets, enhancing effective drug delivery methods, and improving treatment outcomes. We have explored the advantages of utilizing large animal models, particularly pigs, in previous reviews. Since then, however, significant progress has been made in developing more sophisticated animal models that faithfully replicate the typical pathology of HD. In the current review, we provide a comprehensive overview of large animal models of HD, incorporating recent findings regarding the establishment of HD knock-in (KI) pigs and their genetic therapy. We also explore the utilization of large animal models in HD research, with a focus on sheep, non-human primates (NHPs), and pigs. Our objective is to provide valuable insights into the application of these large animal models for the investigation and treatment of neurodegenerative disorders.
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Affiliation(s)
- Bofeng Han
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China
| | - Weien Liang
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China
| | - Xiao-Jiang Li
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China
| | - Shihua Li
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China
| | - Sen Yan
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China. E-mail:
| | - Zhuchi Tu
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-Human Primate Research, Guangzhou, Guangdong 510632, China. E-mail:
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6
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Wang J, Horlacher M, Cheng L, Winther O. DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning. Bioinformatics 2024; 40:btae065. [PMID: 38317052 PMCID: PMC10879750 DOI: 10.1093/bioinformatics/btae065] [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: 12/21/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
MOTIVATION Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information. RESULTS In this article, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localization of RNA molecules via fine-tuning. We constructed DeepLocRNA using a comprehensive dataset with variant RNA types and evaluated it on the held-out dataset. Our model achieved state-of-the-art performance in predicting RNA subcellular localization in mRNA and miRNA. It has also demonstrated great generalization capabilities, performing well on both human and mouse RNA. Additionally, a motif analysis was performed to enhance the interpretability of the model, highlighting signal factors that contributed to the predictions. The proposed model provides general and powerful prediction abilities for different RNA types and species, offering valuable insights into the localization patterns of RNA molecules and contributing to our understanding of cellular processes at the molecular level. A user-friendly web server is available at: https://biolib.com/KU/DeepLocRNA/.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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7
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Driscoll R, Hampton L, Abraham NA, Larigan JD, Joseph NF, Hernandez-Vega JC, Geisler S, Yang FC, Deninger M, Tran DT, Khatri N, Godinho BMDC, Kinberger GA, Montagna DR, Hirst WD, Guardado CL, Glajch KE, Arnold HM, Gallant-Behm CL, Weihofen A. Dose-dependent reduction of somatic expansions but not Htt aggregates by di-valent siRNA-mediated silencing of MSH3 in HdhQ111 mice. Sci Rep 2024; 14:2061. [PMID: 38267530 PMCID: PMC10808119 DOI: 10.1038/s41598-024-52667-3] [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: 11/16/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by CAG trinucleotide repeat expansions in exon 1 of the HTT gene. In addition to germline CAG expansions, somatic repeat expansions in neurons also contribute to HD pathogenesis. The DNA mismatch repair gene, MSH3, identified as a genetic modifier of HD onset and progression, promotes somatic CAG expansions, and thus presents a potential therapeutic target. However, what extent of MSH3 protein reduction is needed to attenuate somatic CAG expansions and elicit therapeutic benefits in HD disease models is less clear. In our study, we employed potent di-siRNAs to silence mouse Msh3 mRNA expression in a dose-dependent manner in HdhQ111/+ mice and correlated somatic Htt CAG instability with MSH3 protein levels from simultaneously isolated DNA and protein after siRNA treatment. Our results reveal a linear correlation with a proportionality constant of ~ 1 between the prevention of somatic Htt CAG expansions and MSH3 protein expression in vivo, supporting MSH3 as a rate-limiting step in somatic expansions. Intriguingly, despite a 75% reduction in MSH3 protein levels, striatal nuclear HTT aggregates remained unchanged. We also note that evidence for nuclear Msh3 mRNA that is inaccessible to RNA interference was found, and that MSH6 protein in the striatum was upregulated following MSH3 knockdown in HdhQ111/+ mice. These results provide important clues to address critical questions for the development of therapeutic molecules targeting MSH3 as a potential therapeutic target for HD.
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Affiliation(s)
- Rachelle Driscoll
- Translational Sciences, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Lucas Hampton
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Neeta A Abraham
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - J Douglas Larigan
- Biotherapeutics and Medicinal Sciences, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Nadine F Joseph
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Juan C Hernandez-Vega
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Sarah Geisler
- Translational Sciences, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Fu-Chia Yang
- Translational Sciences, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Matthew Deninger
- Atalanta Therapeutics, 51 Sleeper Street, Boston, MA, 02210, USA
| | - David T Tran
- Atalanta Therapeutics, 51 Sleeper Street, Boston, MA, 02210, USA
| | - Natasha Khatri
- Atalanta Therapeutics, 51 Sleeper Street, Boston, MA, 02210, USA
| | | | | | - Daniel R Montagna
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Warren D Hirst
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Catherine L Guardado
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Kelly E Glajch
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - H Moore Arnold
- Translational Sciences, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | | | - Andreas Weihofen
- Neurodegenerative Diseases Research Unit, Biogen, 225 Binney Street, Cambridge, MA, 02142, USA.
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8
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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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9
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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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10
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Thompson LM, Orr HT. HD and SCA1: Tales from two 30-year journeys since gene discovery. Neuron 2023; 111:3517-3530. [PMID: 37863037 PMCID: PMC10842341 DOI: 10.1016/j.neuron.2023.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/22/2023]
Abstract
One of the more transformative findings in human genetics was the discovery that the expansion of unstable nucleotide repeats underlies a group of inherited neurological diseases. A subset of these unstable repeat neurodegenerative diseases is due to the expansion of a CAG trinucleotide repeat encoding a stretch of glutamines, i.e., the polyglutamine (polyQ) repeat neurodegenerative diseases. Among the CAG/polyQ repeat diseases are Huntington's disease (HD) and spinocerebellar ataxia type 1 (SCA1), in which the expansions are within widely expressed proteins. Although both HD and SCA1 are autosomal dominantly inherited, and both typically cause mid- to late-life-onset movement disorders with cognitive decline, they each are characterized by distinct clinical characteristics and predominant sites of neuropathology. Importantly, the respective affected proteins, Huntingtin (HTT, HD) and Ataxin 1 (ATXN1, SCA1), have unique functions and biological properties. Here, we review HD and SCA1 with a focus on how their disease-specific and shared features may provide informative insights.
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Affiliation(s)
- Leslie M Thompson
- Department of Psychiatry and Human Behavior, Department of Neurobiology and Behavior, Department of Biological Chemistry, Institute of Memory Impairments and Neurological Disorders, Sue and Bill Gross Stem Cell Center, University of California Irvine, Irvine, CA 92697, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis and Saint Paul, MN 55455, USA.
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11
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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12
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Gantley L, Stringer BW, Conn VM, Ootsuka Y, Holds D, Slee M, Aliakbari K, Kirk K, Ormsby RJ, Webb ST, Hanson A, Lin H, Selth LA, Conn SJ. Functional Characterisation of the Circular RNA, circHTT(2-6), in Huntington's Disease. Cells 2023; 12:cells12091337. [PMID: 37174737 PMCID: PMC10177161 DOI: 10.3390/cells12091337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Trinucleotide repeat disorders comprise ~20 severe, inherited, human neuromuscular and neurodegenerative disorders, which result from an abnormal expansion of repetitive sequences in the DNA. The most common of these, Huntington's disease (HD), results from expansion of the CAG repeat region in exon 1 of the HTT gene via an unknown mechanism. Since non-coding RNAs have been implicated in the initiation and progression of many diseases, herein we focused on a circular RNA (circRNA) molecule arising from non-canonical splicing (backsplicing) of HTT pre-mRNA. The most abundant circRNA from HTT, circHTT(2-6), was found to be more highly expressed in the frontal cortex of HD patients, compared with healthy controls, and positively correlated with CAG repeat tract length. Furthermore, the mouse orthologue (mmu_circHTT(2-6)) was found to be enriched within the brain and specifically the striatum, a region enriched for medium spiny neurons that are preferentially lost in HD. Transgenic overexpression of circHTT(2-6) in two human cell lines-SH-SY5Y and HEK293-reduced cell proliferation and nuclear size without affecting cell cycle progression or cellular size, or altering the CAG repeat region length within HTT. CircHTT(2-6) overexpression did not alter total HTT protein levels, but reduced its nuclear localisation. As these phenotypic and genotypic changes resemble those observed in HD patients, our results suggest that circHTT(2-6) may play a functional role in the pathophysiology of this disease.
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Affiliation(s)
- Laura Gantley
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Brett W Stringer
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
- Lifelong Health, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Vanessa M Conn
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Youichirou Ootsuka
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
- Centre for Neuroscience, Human Physiology, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Duncan Holds
- Department of Genetics and Molecular Pathology, SA Pathology, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Mark Slee
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Kamelya Aliakbari
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Kirsty Kirk
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Rebecca J Ormsby
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Stuart T Webb
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Adrienne Hanson
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - He Lin
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Luke A Selth
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA 5042, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Simon J Conn
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
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13
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Gabanella F, Onori A, Pisani C, Fiore M, Ferraguti G, Colizza A, de Vincentiis M, Ceccanti M, Inghilleri M, Corbi N, Passananti C, Di Certo MG. SMN Deficiency Destabilizes ABCA1 Expression in Human Fibroblasts: Novel Insights in Pathophysiology of Spinal Muscular Atrophy. Int J Mol Sci 2023; 24:ijms24032916. [PMID: 36769246 PMCID: PMC9917534 DOI: 10.3390/ijms24032916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The deficiency of survival motor neuron protein (SMN) causes spinal muscular atrophy (SMA), a rare neuromuscular disease that affects different organs. SMN is a key player in RNA metabolism regulation. An intriguing aspect of SMN function is its relationship with plasma membrane-associated proteins. Here, we provide a first demonstration that SMN affects the ATP-binding cassette transporter A1, (ABCA1), a membrane protein critically involved in cholesterol homeostasis. In human fibroblasts, we showed that SMN associates to ABCA1 mRNA, and impacts its subcellular distribution. Consistent with the central role of ABCA1 in the efflux of free cholesterol from cells, we observed a cholesterol accumulation in SMN-depleted human fibroblasts. These results were also confirmed in SMA type I patient-derived fibroblasts. These findings not only validate the intimate connection between SMN and plasma membrane-associated proteins, but also highlight a contribution of dysregulated cholesterol efflux in SMA pathophysiology.
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Affiliation(s)
- Francesca Gabanella
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
- Correspondence: (F.G.); (M.G.D.C.)
| | - Annalisa Onori
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Cinzia Pisani
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Marco Fiore
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
| | - Andrea Colizza
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
| | - Marco de Vincentiis
- Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
| | - Marco Ceccanti
- Center for Rare Neuromuscular Diseases, Department of Human Neuroscience, Policlinico Umberto I, Sapienza University of Rome, 00185 Rome, Italy
| | - Maurizio Inghilleri
- Center for Rare Neuromuscular Diseases, Department of Human Neuroscience, Policlinico Umberto I, Sapienza University of Rome, 00185 Rome, Italy
| | - Nicoletta Corbi
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Claudio Passananti
- CNR-Institute of Molecular Biology and Pathology, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy
| | - Maria Grazia Di Certo
- CNR-Institute of Biochemistry and Cell Biology, Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy
- Correspondence: (F.G.); (M.G.D.C.)
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14
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Joachimiak P, Ciesiołka A, Kozłowska E, Świtoński PM, Figura G, Ciołak A, Adamek G, Surdyka M, Kalinowska-Pośka Ż, Figiel M, Caron NS, Hayden MR, Fiszer A. Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models. BMC Biol 2023; 21:17. [PMID: 36726088 PMCID: PMC9893648 DOI: 10.1186/s12915-023-01515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The majority of genes in the human genome is present in two copies but the expression levels of both alleles is not equal. Allelic imbalance is an aspect of gene expression relevant not only in the context of genetic variation, but also to understand the pathophysiology of genes implicated in genetic disorders, in particular, dominant genetic diseases where patients possess one normal and one mutant allele. Polyglutamine (polyQ) diseases are caused by the expansion of CAG trinucleotide tracts within specific genes. Spinocerebellar ataxia type 3 (SCA3) and Huntington's disease (HD) patients harbor one normal and one mutant allele that differ in the length of CAG tracts. However, assessing the expression level of individual alleles is challenging due to the presence of abundant CAG repeats in the human transcriptome, which make difficult the design of allele-specific methods, as well as of therapeutic strategies to selectively engage CAG sequences in mutant transcripts. RESULTS To precisely quantify expression in an allele-specific manner, we used SNP variants that are linked to either normal or CAG expanded alleles of the ataxin-3 (ATXN3) and huntingtin (HTT) genes in selected patient-derived cell lines. We applied a SNP-based quantitative droplet digital PCR (ddPCR) protocol for precise determination of the levels of transcripts in cellular and mouse models. For HD, we showed that the process of cell differentiation can affect the ratio between endogenous alleles of HTT mRNA. Additionally, we reported changes in the absolute number of the ATXN3 and HTT transcripts per cell during neuronal differentiation. We also implemented our assay to reliably monitor, in an allele-specific manner, the silencing efficiency of mRNA-targeting therapeutic approaches for HD. Finally, using the humanized Hu128/21 HD mouse model, we showed that the ratio of normal and mutant HTT transgene expression in brain slightly changes with the age of mice. CONCLUSIONS Using allele-specific ddPCR assays, we observed differences in allele expression levels in the context of SCA3 and HD. Our allele-selective approach is a reliable and quantitative method to analyze low abundant transcripts and is performed with high accuracy and reproducibility. Therefore, the use of this approach can significantly improve understanding of allele-related mechanisms, e.g., related with mRNA processing that may be affected in polyQ diseases.
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Affiliation(s)
- Paweł Joachimiak
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiołka
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Emilia Kozłowska
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paweł M. Świtoński
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Grzegorz Figura
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agata Ciołak
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Grażyna Adamek
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Magdalena Surdyka
- grid.413454.30000 0001 1958 0162Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Żaneta Kalinowska-Pośka
- grid.413454.30000 0001 1958 0162Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Figiel
- grid.413454.30000 0001 1958 0162Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Nicholas S. Caron
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Michael R. Hayden
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Agnieszka Fiszer
- grid.413454.30000 0001 1958 0162Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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15
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Fienko S, Landles C, Sathasivam K, McAteer SJ, Milton RE, Osborne GF, Smith EJ, Jones ST, Bondulich MK, Danby ECE, Phillips J, Taxy BA, Kordasiewicz HB, Bates GP. Alternative processing of human HTT mRNA with implications for Huntington's disease therapeutics. Brain 2022; 145:4409-4424. [PMID: 35793238 PMCID: PMC9762945 DOI: 10.1093/brain/awac241] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/17/2022] [Accepted: 06/11/2022] [Indexed: 11/14/2022] Open
Abstract
Huntington disease is caused by a CAG repeat expansion in exon 1 of the huntingtin gene (HTT) that is translated into a polyglutamine stretch in the huntingtin protein (HTT). We previously showed that HTT mRNA carrying an expanded CAG repeat was incompletely spliced to generate HTT1a, an exon 1 only transcript, which was translated to produce the highly aggregation-prone and pathogenic exon 1 HTT protein. This occurred in all knock-in mouse models of Huntington's disease and could be detected in patient cell lines and post-mortem brains. To extend these findings to a model system expressing human HTT, we took advantage of YAC128 mice that are transgenic for a yeast artificial chromosome carrying human HTT with an expanded CAG repeat. We discovered that the HTT1a transcript could be detected throughout the brains of YAC128 mice. We implemented RNAscope to visualize HTT transcripts at the single molecule level and found that full-length HTT and HTT1a were retained together in large nuclear RNA clusters, as well as being present as single transcripts in the cytoplasm. Homogeneous time-resolved fluorescence analysis demonstrated that the HTT1a transcript had been translated to produce the exon 1 HTT protein. The levels of exon 1 HTT in YAC128 mice, correlated with HTT aggregation, supportive of the hypothesis that exon 1 HTT initiates the aggregation process. Huntingtin-lowering strategies are a major focus of therapeutic development for Huntington's disease. These approaches often target full-length HTT alone and would not be expected to reduce pathogenic exon 1 HTT levels. We have established YAC128 mouse embryonic fibroblast lines and shown that, together with our QuantiGene multiplex assay, these provide an effective screening tool for agents that target HTT transcripts. The effects of current targeting strategies on nuclear RNA clusters are unknown, structures that may have a pathogenic role or alternatively could be protective by retaining HTT1a in the nucleus and preventing it from being translated. In light of recently halted antisense oligonucleotide trials, it is vital that agents targeting HTT1a are developed, and that the effects of HTT-lowering strategies on the subcellular levels of all HTT transcripts and their various HTT protein isoforms are understood.
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Affiliation(s)
- Sandra Fienko
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Christian Landles
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Kirupa Sathasivam
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Sean J McAteer
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Rebecca E Milton
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Georgina F Osborne
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Edward J Smith
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Samuel T Jones
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Marie K Bondulich
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Emily C E Danby
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Jemima Phillips
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | - Bridget A Taxy
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
| | | | - Gillian P Bates
- Department of Neurodegenerative Disease, Huntington’s Disease Centre and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, UCL, London WC1N 3BG, UK
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16
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Isiktas AU, Eshov A, Yang S, Guo JU. Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. CELL REPORTS METHODS 2022; 2:100334. [PMID: 36452875 PMCID: PMC9701603 DOI: 10.1016/j.crmeth.2022.100334] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
A common pathological feature of RNAs containing expanded repeat sequences is their propensity to aggregate in cells. While some repeat RNA aggregates have been shown to cause toxicity by sequestering RNA-binding proteins, the molecular mechanism of aggregation remains unclear. Here, we devised an efficient method to generate long tandem repeat DNAs de novo and applied it to systematically determine the sequence features underlying RNA aggregation. Live-cell imaging of repeat RNAs indicated that aggregation was promoted by multivalent RNA-RNA interactions via either canonical or noncanonical base pairs. While multiple runs of two consecutive base pairs were sufficient, longer runs of base pairs such as those formed by GGGGCC hexanucleotide repeats further enhanced aggregation. In summary, our study provides a unifying model for the molecular basis of repeat RNA aggregation and a generalizable approach for identifying the sequence and structural determinants underlying the distinct properties of repeat DNAs and RNAs.
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Affiliation(s)
- Atagun U. Isiktas
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Aziz Eshov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzhou Yang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
| | - Junjie U. Guo
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
- Interdepartmental Neuroscience Program, Yale University, New Haven, CT 06520, USA
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17
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Ly S, Didiot MC, Ferguson CM, Coles AH, Miller R, Chase K, Echeverria D, Wang F, Sadri-Vakili G, Aronin N, Khvorova A. Mutant huntingtin messenger RNA forms neuronal nuclear clusters in rodent and human brains. Brain Commun 2022; 4:fcac248. [PMID: 36458209 PMCID: PMC9707646 DOI: 10.1093/braincomms/fcac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/14/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023] Open
Abstract
Mutant messenger RNA (mRNA) and protein contribute to the clinical manifestation of many repeat-associated neurological disorders, with the presence of nuclear RNA clusters being a common pathological feature. Yet, investigations into Huntington's disease-caused by a CAG repeat expansion in exon 1 of the huntingtin (HTT) gene-have primarily focused on toxic protein gain-of-function as the primary disease-causing feature. To date, mutant HTT mRNA has not been identified as an in vivo hallmark of Huntington's disease. Here, we report that, in two Huntington's disease mouse models (YAC128 and BACHD-97Q-ΔN17), mutant HTT mRNA is retained in the nucleus. Widespread formation of large mRNA clusters (∼0.6-5 µm3) occurred in 50-75% of striatal and cortical neurons. Cluster formation was independent of age and driven by expanded repeats. Clusters associate with chromosomal transcriptional sites and quantitatively co-localize with the aberrantly processed N-terminal exon 1-intron 1 mRNA isoform, HTT1a. HTT1a mRNA clusters are observed in a subset of neurons from human Huntington's disease post-mortem brain and are likely caused by somatic expansion of repeats. In YAC128 mice, clusters, but not individual HTT mRNA, are resistant to antisense oligonucleotide treatment. Our findings identify mutant HTT/HTT1a mRNA clustering as an early, robust molecular signature of Huntington's disease, providing in vivo evidence that Huntington's disease is a repeat expansion disease with mRNA involvement.
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Affiliation(s)
| | | | | | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kathryn Chase
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Feng Wang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Ghazaleh Sadri-Vakili
- Mass General Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neil Aronin
- Correspondence may also be addressed to: Neil Aronin 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA. E-mail:
| | - Anastasia Khvorova
- Correspondence to: Anastasia Khvorova 368 Plantation Street, Albert Sherman Center Worcester, MA 01655, USA E-mail:
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18
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EL-RMLocNet: An Explainable LSTM Network for RNA-Associated Multi-Compartment Localization Prediction. Comput Struct Biotechnol J 2022; 20:3986-4002. [PMID: 35983235 PMCID: PMC9356161 DOI: 10.1016/j.csbj.2022.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 11/23/2022] Open
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Molecular Pathophysiological Mechanisms in Huntington's Disease. Biomedicines 2022; 10:biomedicines10061432. [PMID: 35740453 PMCID: PMC9219859 DOI: 10.3390/biomedicines10061432] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
Huntington’s disease is an inherited neurodegenerative disease described 150 years ago by George Huntington. The genetic defect was identified in 1993 to be an expanded CAG repeat on exon 1 of the huntingtin gene located on chromosome 4. In the following almost 30 years, a considerable amount of research, using mainly animal models or in vitro experiments, has tried to unravel the complex molecular cascades through which the transcription of the mutant protein leads to neuronal loss, especially in the medium spiny neurons of the striatum, and identified excitotoxicity, transcriptional dysregulation, mitochondrial dysfunction, oxidative stress, impaired proteostasis, altered axonal trafficking and reduced availability of trophic factors to be crucial contributors. This review discusses the pathogenic cascades described in the literature through which mutant huntingtin leads to neuronal demise. However, due to the ubiquitous presence of huntingtin, astrocytes are also dysfunctional, and neuroinflammation may additionally contribute to Huntington’s disease pathology. The quest for therapies to delay the onset and reduce the rate of Huntington’s disease progression is ongoing, but is based on findings from basic research.
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Gu X, Richman J, Langfelder P, Wang N, Zhang S, Bañez-Coronel M, Wang HB, Yang L, Ramanathan L, Deng L, Park CS, Choi CR, Cantle JP, Gao F, Gray M, Coppola G, Bates GP, Ranum LPW, Horvath S, Colwell CS, Yang XW. Uninterrupted CAG repeat drives striatum-selective transcriptionopathy and nuclear pathogenesis in human Huntingtin BAC mice. Neuron 2022; 110:1173-1192.e7. [PMID: 35114102 PMCID: PMC9462388 DOI: 10.1016/j.neuron.2022.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/30/2021] [Accepted: 01/06/2022] [Indexed: 02/08/2023]
Abstract
In Huntington's disease (HD), the uninterrupted CAG repeat length, but not the polyglutamine length, predicts disease onset. However, the underlying pathobiology remains unclear. Here, we developed bacterial artificial chromosome (BAC) transgenic mice expressing human mutant huntingtin (mHTT) with uninterrupted, and somatically unstable, CAG repeats that exhibit progressive disease-related phenotypes. Unlike prior mHTT transgenic models with stable, CAA-interrupted, polyglutamine-encoding repeats, BAC-CAG mice show robust striatum-selective nuclear inclusions and transcriptional dysregulation resembling those in murine huntingtin knockin models and HD patients. Importantly, the striatal transcriptionopathy in HD models is significantly correlated with their uninterrupted CAG repeat length but not polyglutamine length. Finally, among the pathogenic entities originating from mHTT genomic transgenes and only present or enriched in the uninterrupted CAG repeat model, somatic CAG repeat instability and nuclear mHTT aggregation are best correlated with early-onset striatum-selective molecular pathogenesis and locomotor and sleep deficits, while repeat RNA-associated pathologies and repeat-associated non-AUG (RAN) translation may play less selective or late pathogenic roles, respectively.
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Affiliation(s)
- Xiaofeng Gu
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey Richman
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Langfelder
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nan Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shasha Zhang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Monica Bañez-Coronel
- Center for Neurogenetics, Department of Molecular Genetics and Microbiology, College of Medicine, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute of Neurological Diseases, University of Florida, Gainesville, FL, USA
| | - Huei-Bin Wang
- Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lucia Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lalini Ramanathan
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Linna Deng
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chang Sin Park
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher R Choi
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey P Cantle
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fuying Gao
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michelle Gray
- Department of Neurology and Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Giovanni Coppola
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gillian P Bates
- Huntington's Disease Centre, Sobell Department of Motor Neuroscience and Movement Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Laura P W Ranum
- Center for Neurogenetics, Department of Molecular Genetics and Microbiology, College of Medicine, Genetics Institute, McKnight Brain Institute, Norman Fixel Institute of Neurological Diseases, University of Florida, Gainesville, FL, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher S Colwell
- Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department Psychiatry and Biobehavioral Science, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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Trujillo-Del Río C, Tortajada-Pérez J, Gómez-Escribano AP, Casterá F, Peiró C, Millán JM, Herrero MJ, Vázquez-Manrique RP. Metformin to treat Huntington disease: a pleiotropic drug against a multi-system disorder. Mech Ageing Dev 2022; 204:111670. [DOI: 10.1016/j.mad.2022.111670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/17/2022]
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22
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Savulescu AF, Bouilhol E, Beaume N, Nikolski M. Prediction of RNA subcellular localization: Learning from heterogeneous data sources. iScience 2021; 24:103298. [PMID: 34765919 PMCID: PMC8571491 DOI: 10.1016/j.isci.2021.103298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA subcellular localization has recently emerged as a widespread phenomenon, which may apply to the majority of RNAs. The two main sources of data for characterization of RNA localization are sequence features and microscopy images, such as obtained from single-molecule fluorescent in situ hybridization-based techniques. Although such imaging data are ideal for characterization of RNA distribution, these techniques remain costly, time-consuming, and technically challenging. Given these limitations, imaging data exist only for a limited number of RNAs. We argue that the field of RNA localization would greatly benefit from complementary techniques able to characterize location of RNA. Here we discuss the importance of RNA localization and the current methodology in the field, followed by an introduction on prediction of location of molecules. We then suggest a machine learning approach based on the integration between imaging localization data and sequence-based data to assist in characterization of RNA localization on a transcriptome level.
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Affiliation(s)
- Anca Flavia Savulescu
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925 Cape Town, South Africa
| | - Emmanuel Bouilhol
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
| | - Nicolas Beaume
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town,7925 Cape Town, South Africa
| | - Macha Nikolski
- Université de Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux, France
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Jarosińska OD, Rüdiger SGD. Molecular Strategies to Target Protein Aggregation in Huntington's Disease. Front Mol Biosci 2021; 8:769184. [PMID: 34869596 PMCID: PMC8636123 DOI: 10.3389/fmolb.2021.769184] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by the aggregation of the mutant huntingtin (mHTT) protein in nerve cells. mHTT self-aggregates to form soluble oligomers and insoluble fibrils, which interfere in a number of key cellular functions. This leads to cell quiescence and ultimately cell death. There are currently still no treatments available for HD, but approaches targeting the HTT levels offer systematic, mechanism-driven routes towards curing HD and other neurodegenerative diseases. This review summarizes the current state of knowledge of the mRNA targeting approaches such as antisense oligonucleotides and RNAi system; and the novel methods targeting mHTT and aggregates for degradation via the ubiquitin proteasome or the autophagy-lysosomal systems. These methods include the proteolysis-targeting chimera, Trim-Away, autophagosome-tethering compound, autophagy-targeting chimera, lysosome-targeting chimera and approach targeting mHTT for chaperone-mediated autophagy. These molecular strategies provide a knowledge-based approach to target HD and other neurodegenerative diseases at the origin.
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Affiliation(s)
- Olga D. Jarosińska
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Science for Life, Utrecht University, Utrecht, Netherlands
| | - Stefan G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Science for Life, Utrecht University, Utrecht, Netherlands
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24
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Glineburg MR, Zhang Y, Krans A, Tank EM, Barmada SJ, Todd PK. Enhanced detection of expanded repeat mRNA foci with hybridization chain reaction. Acta Neuropathol Commun 2021; 9:73. [PMID: 33892814 PMCID: PMC8063431 DOI: 10.1186/s40478-021-01169-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transcribed nucleotide repeat expansions form detectable RNA foci in patient cells that contribute to disease pathogenesis. The most widely used method for detecting RNA foci, fluorescence in situ hybridization (FISH), is powerful but can suffer from issues related to signal above background. Here we developed a repeat-specific form of hybridization chain reaction (R-HCR) as an alternative method for detection of repeat RNA foci in two neurodegenerative disorders: C9orf72 associated ALS and frontotemporal dementia (C9 ALS/FTD) and Fragile X-associated tremor/ataxia syndrome. R-HCR to both G4C2 and CGG repeats exhibited comparable specificity but > 40 × sensitivity compared to FISH, with better detection of both nuclear and cytoplasmic foci in human C9 ALS/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. Using R-HCR, we observed that integrated stress response (ISR) activation significantly increased the number of endogenous G4C2 repeat RNA foci and triggered their selective nuclear accumulation without evidence of stress granule co-localization in patient fibroblasts and patient derived neurons. These data suggest that R-HCR can be a useful tool for tracking the behavior of repeat expansion mRNA in C9 ALS/FTD and other repeat expansion disorders.
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25
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Shiyanbola O, Hardin H, Hu R, Eickhoff JC, Lloyd RV. Long Noncoding RNA Expression in Adrenal Cortical Neoplasms. Endocr Pathol 2020; 31:385-391. [PMID: 32725507 DOI: 10.1007/s12022-020-09642-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2020] [Indexed: 12/29/2022]
Abstract
Long noncoding RNAs (lncRNAs) consist of nucleic acid molecules that are greater than 200 nucleotides in length and they do not code for specific proteins. A growing body of evidence indicates that these lncRNAs have important roles in tumorigenesis. Separating adrenal cortical adenomas from carcinomas is often a difficult problem for the surgical pathologist. This is especially true when only small needle biopsies are available for examination. We used in situ hybridization (ISH) analysis to study normal adrenal cortical tissues and adrenal cortical tumors to determine the role of specific lncRNAs in tumor development and classification. The lncRNAS studied included metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), psoriasis susceptibility-related RNA gene induced by stress (PRINS), and HOX antisense intergenic RNA myeloid 1 (HAM1). We constructed a tissue microarray (TMA) for the studies and also analyzed a subset of cases by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Two 1-mm duplicate cores of normal adrenal cortex (NAC) (n = 23), adrenal cortical adenomas (ACAs) (n = 95), and adrenal cortical carcinomas (ACCs), (n = 20) were used on the TMA. The results of ISH were analyzed by image analysis. ISH showed predominantly nuclear expression of lncRNAs in adrenal cortical tissues. MALAT1 showed more expression in ACCs than in NAC and ACA (p < 0.05). PRINS had higher expression in NACs and ACAs than in ACCs. The lncRNAs MALAT1, PRINS, and HAM1 are all expressed in normal and neoplastic adrenal cortical tissues. MALAT1 had the highest expression in ACC compared to ACAs and may have a role in ACC development.
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Affiliation(s)
- Oyewale Shiyanbola
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Heather Hardin
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Rong Hu
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jens C Eickhoff
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ricardo V Lloyd
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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26
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SMN protein promotes membrane compartmentalization of ribosomal protein S6 transcript in human fibroblasts. Sci Rep 2020; 10:19000. [PMID: 33149163 PMCID: PMC7643083 DOI: 10.1038/s41598-020-76174-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Alterations of RNA homeostasis can lead to severe pathological conditions. The Survival of Motor Neuron (SMN) protein, which is reduced in Spinal Muscular Atrophy, impacts critical aspects of the RNA life cycle, such as splicing, trafficking, and translation. Increasing evidence points to a potential role of SMN in ribosome biogenesis. Our previous study revealed that SMN promotes membrane-bound ribosomal proteins (RPs), sustaining activity-dependent local translation. Here, we suggest that plasma membrane domains could be a docking site not only for RPs but also for their encoding transcripts. We have shown that SMN knockdown perturbs subcellular localization as well as translation efficiency of RPS6 mRNA. We have also shown that plasma membrane-enriched fractions from human fibroblasts retain RPS6 transcripts in an SMN-dependent manner. Furthermore, we revealed that SMN traffics with RPS6 mRNA promoting its association with caveolin-1, a key component of membrane dynamics. Overall, these findings further support the SMN-mediated crosstalk between plasma membrane dynamics and translation machinery. Importantly, our study points to a potential role of SMN in the ribosome assembly pathway by selective RPs synthesis/localization in both space and time.
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27
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Boumil EF, Castro N, Phillips AT, Chatterton JE, McCauley SM, Wolfson AD, Shmushkovich T, Ridilla M, Bernstein AM. USP10 Targeted Self-Deliverable siRNA to Prevent Scarring in the Cornea. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:1029-1043. [PMID: 32829179 PMCID: PMC7452140 DOI: 10.1016/j.omtn.2020.07.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/17/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023]
Abstract
Ocular scarring after surgery, trauma, or infection leads to vision loss. The transparent cornea is an excellent model system to test anti-scarring therapies. Cholesterol-conjugated fully modified asymmetric small interfering RNAs (siRNAs) (self-deliverable siRNAs [sdRNAs]) are a novel modality for in vivo gene knockdown, transfecting cells and tissues without any additional formulations. Myofibroblasts are a main contributor to scarring and fibrosis. αv integrins play a central role in myofibroblast pathological adhesion, overcontraction, and transforming growth factor β (TGF-β) activation. Previously, we demonstrated that αv integrins are protected from intracellular degradation after wounding by upregulation of the deubiquitinase (DUB) ubiquitin-specific protease 10 (USP10), leading to integrin cell surface accumulation. In this study, we tested whether knockdown of USP10 with a USP10-targeting sdRNA (termed US09) will reduce scarring after wounding a rabbit cornea in vivo. The wounded corneal stroma was treated once with US09 or non-targeting control (NTC) sdRNA. At 6 weeks US09 treatment resulted in faster wound closure, limited scarring, and suppression of fibrotic markers and immune response. Specifically, fibronectin-extra domain A (EDA), collagen III, and a-smooth muscle actin (p < 0.05), CD45+ cell infiltration (p < 0.01), and apoptosis at 24 (p < 0.01) and 48 h (p < 0.05) were reduced post-wounding. Corneal thickness and cell proliferation were restored to unwounded parameters. Targeting the DUB, USP10 is a novel strategy to reduce scarring. This study indicates that ubiquitin-mediated pathways should be considered in the pathogenesis of fibrotic healing.
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Affiliation(s)
- Edward F Boumil
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Nileyma Castro
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Andrew T Phillips
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | | | | | | | | | - Marc Ridilla
- Repair Biotechnologies, 841 East Fayette Street, Syracuse, NY 13210, USA
| | - Audrey M Bernstein
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.
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Ferguson CM, Echeverria D, Hassler M, Ly S, Khvorova A. Cell Type Impacts Accessibility of mRNA to Silencing by RNA Interference. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:384-393. [PMID: 32650236 PMCID: PMC7340969 DOI: 10.1016/j.omtn.2020.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/04/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
RNA interference (RNAi) is a potent mechanism that silences mRNA and protein expression in all cells and tissue types. RNAi is known to exert many of its functional effects in the cytoplasm, and thus, the cellular localization of target mRNA may impact observed potency. Here, we demonstrate that cell identity has a profound impact on accessibility of apolipoprotein E (ApoE) mRNA to RNAi. We show that, whereas both neuronal and glial cell lines express detectable ApoE mRNA, in neuronal cells, ApoE mRNA is not targetable by RNAi. Screening of a panel of thirty-five chemically modified small interfering RNAs (siRNAs) did not produce a single hit in a neuronal cell line, whereas up to fifteen compounds showed strong efficacy in glial cells. Further investigation of the cellular localization of ApoE mRNA demonstrates that ApoE mRNA is partially spliced and preferentially localized to the nucleus (∼80%) in neuronal cells, whereas more than 90% of ApoE mRNA is cytoplasmic in glial cells. Such an inconsistency in intracellular localization and splicing might provide an explanation for functional differences in RNAi compounds. Thus, cellular origin might have an impact on accessibility of mRNA to RNAi and should be taken into account during the screening process.
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Affiliation(s)
- Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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29
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Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. Cell Mol Life Sci 2020; 78:1577-1596. [PMID: 32696070 PMCID: PMC7904544 DOI: 10.1007/s00018-020-03596-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
Polyglutamine (polyQ) diseases are incurable neurological disorders caused by CAG repeat expansion in the open reading frames (ORFs) of specific genes. This type of mutation in the HTT gene is responsible for Huntington’s disease (HD). CAG repeat-targeting artificial miRNAs (art-miRNAs) were shown as attractive therapeutic approach for polyQ disorders as they caused allele-selective decrease in the level of mutant proteins. Here, using polyQ disease models, we aimed to demonstrate how miRNA-based gene expression regulation is dependent on target sequence features. We show that the silencing efficiency and selectivity of art-miRNAs is influenced by the localization of the CAG repeat tract within transcript and the specific sequence context. Furthermore, we aimed to reveal the events leading to downregulation of mutant polyQ proteins and found very rapid activation of translational repression and HTT transcript deadenylation. Slicer-activity of AGO2 was dispensable in this process, as determined in AGO2 knockout cells generated with CRISPR-Cas9 technology. We also showed highly allele-selective downregulation of huntingtin in human HD neural progenitors (NPs). Taken together, art-miRNA activity may serve as a model of the cooperative activity and targeting of ORF regions by endogenous miRNAs.
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Zhang ZY, Yang YH, Ding H, Wang D, Chen W, Lin H. Design powerful predictor for mRNA subcellular location prediction in Homo sapiens. Brief Bioinform 2020; 22:526-535. [PMID: 31994694 DOI: 10.1093/bib/bbz177] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022] Open
Abstract
Messenger RNAs (mRNAs) shoulder special responsibilities that transmit genetic code from DNA to discrete locations in the cytoplasm. The locating process of mRNA might provide spatial and temporal regulation of mRNA and protein functions. The situ hybridization and quantitative transcriptomics analysis could provide detail information about mRNA subcellular localization; however, they are time consuming and expensive. It is highly desired to develop computational tools for timely and effectively predicting mRNA subcellular location. In this work, by using binomial distribution and one-way analysis of variance, the optimal nonamer composition was obtained to represent mRNA sequences. Subsequently, a predictor based on support vector machine was developed to identify the mRNA subcellular localization. In 5-fold cross-validation, results showed that the accuracy is 90.12% for Homo sapiens (H. sapiens). The predictor may provide a reference for the study of mRNA localization mechanisms and mRNA translocation strategies. An online web server was established based on our models, which is available at http://lin-group.cn/server/iLoc-mRNA/.
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Affiliation(s)
- Zhao-Yue Zhang
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Yu-He Yang
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hui Ding
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Dong Wang
- Department of Bioinformatics at Southern Medical University
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy at Chengdu University of Traditional Chinese Medicine
| | - Hao Lin
- Center for Informational Biology at University of Electronic Science and Technology of China
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31
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A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nat Biotechnol 2019; 37:884-894. [PMID: 31375812 PMCID: PMC6879195 DOI: 10.1038/s41587-019-0205-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Sustained silencing of gene expression in deep regions of the brain using small interfering RNAs (siRNAs) has not been achieved. Here we describe an siRNA architecture, divalent-siRNA (Di-siRNA), that supports potent, sustained gene silencing in the central nervous system (CNS) of mice and non-human primates following a single injection into cerebrospinal fluid. Di-siRNAs are composed of two fully chemically modified, phosphorothioate-containing siRNAs connected by a linker. In mice, Di-siRNAs induced potent silencing of huntingtin, the causative gene in Huntington’s disease, reducing mRNA and protein throughout the brain. Silencing persisted for at least six months, with the degree of gene silencing correlating to guide strand tissue accumulation levels. In Cynomolgus macaques, a bolus injection of Di-siRNA showed substantial distribution and robust silencing throughout the brain and spinal cord without detectable toxicity and with minimal off-target effects. This siRNA design may enable RNAi-based gene silencing in the CNS for the treatment of neurological disorders.
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32
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Abstract
Nucleotide repeat disorders encompass more than 30 diseases, most of which show dominant inheritance, such as Huntington's disease, spinocerebellar ataxias, and myotonic dystrophies. Yet others, including Friedreich's ataxia, are recessively inherited. A common feature is the presence of a DNA tandem repeat in the disease-associated gene and the propensity of the repeats to expand in germ and in somatic cells, with ensuing neurological and frequently also neuromuscular defects. Repeat expansion is the most frequent event in these diseases; however, sequence contractions, deletions, and mutations have also been reported. Nucleotide repeat sequences are predisposed to adopt non-B-DNA conformations, such as hairpins, cruciform, and intramolecular triple-helix structures (triplexes), also known as H-DNA. For gain-of-function disorders, oligonucleotides can be used to target either transcripts or duplex DNA and in diseases with recessive inheritance oligonucleotides may be used to alter repressive DNA or RNA conformations. Most current treatment strategies are aimed at altering transcript levels, but therapies directed against DNA are also emerging, and novel strategies targeting DNA, instead of RNA, are described. Different mechanisms using modified oligonucleotides are discussed along with the structural aspects of repeat sequences, which can influence binding modes and efficiencies.
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Affiliation(s)
- Rula Zain
- Department of Laboratory Medicine, Centre for Advanced Therapies, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Centre for Advanced Therapies, Karolinska Institutet, Karolinska University Hospital, SE-141 86, Stockholm, Sweden
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