1
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Wang PY, Bartel DP. The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. Mol Cell 2024; 84:2918-2934.e11. [PMID: 39025072 DOI: 10.1016/j.molcel.2024.06.026] [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: 09/26/2023] [Revised: 05/03/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that, for different guide-RNA sequences, slicing rates of perfectly complementary bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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2
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Ferguson CM, Sapp E, Fakih HH, Tang Q, Yamada N, Furgal RC, Paquette JD, Biscans A, Bramato BM, McHugh N, Summers A, Lochmann C, Godinho BMDC, Hildebrand S, Jackson SO, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Enhancing siRNA efficacy in vivo with extended nucleic acid backbones. Nat Biotechnol 2024:10.1038/s41587-024-02336-7. [PMID: 39090305 DOI: 10.1038/s41587-024-02336-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/25/2024] [Indexed: 08/04/2024]
Abstract
Therapeutic small interfering RNA (siRNA) requires sugar and backbone modifications to inhibit nuclease degradation. However, metabolic stabilization by phosphorothioate (PS), the only backbone chemistry used clinically, may be insufficient for targeting extrahepatic tissues. To improve oligonucleotide stabilization, we report the discovery, synthesis and characterization of extended nucleic acid (exNA) consisting of a methylene insertion between the 5'-C and 5'-OH of a nucleoside. exNA incorporation is compatible with common oligonucleotide synthetic protocols and the PS backbone, provides stabilization against 3' and 5' exonucleases and is tolerated at multiple oligonucleotide positions. A combined exNA-PS backbone enhances resistance to 3' exonuclease by ~32-fold over the conventional PS backbone and by >1,000-fold over the natural phosphodiester backbone, improving tissue exposure, tissue accumulation and efficacy in mice, both systemically and in the brain. The improved efficacy and durability imparted by exNA may enable therapeutic interventions in extrahepatic tissues, both with siRNA and with other oligonucleotides such as CRISPR guide RNA, antisense oligonucleotides, mRNA and tRNA.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Vignesh N Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Raymond C Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Joseph D Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Brianna M Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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3
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Sarapata K, Kania A. Revealing miRNAs patterns by employing matrix representations and energy analysis. J Mol Graph Model 2024; 132:108835. [PMID: 39106629 DOI: 10.1016/j.jmgm.2024.108835] [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: 06/24/2023] [Revised: 07/16/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression. Despite their relatively short length (about 21 nucleotides), they can regulate thousands of transcripts within a cell. Due to their low complementarity to targets, studying their activity and binding region preferences (3'UTR, 5'UTR, or CDS) is challenging. In this paper, we analyzed a set of human miRNAs to uncover their general patterns. We began with a sequence logo to verify conservation at specific positions. To discover long-range correlations, we employed chaos game representation (CGR) and genomatrix, methods that enable both graphical and analytical analysis of sequence sets and are well-established in bioinformatics. Our results showed that miRNAs exhibit strongly non-random and characteristic patterns. To incorporate physicochemical properties into the analysis, we applied the electron-ion interaction potential (EIIP) parameter. An important part of our study was to validate the division of miRNAs into two parts-seed and puzzle. The seed region is responsible for target binding, while the puzzle region likely interacts with the RISC complex. We estimated duplex binding energy within the 3'UTR, 5'UTR, and CDS regions using the miRanda tool. Based on the median energy distribution, we divided the miRNAs into two subsets, reflecting different patterns in chaos game representation. Interestingly, one subset displayed significant similarity to conserved and highly confidential miRNAs. Our results confirm the low complementarity of miRNA/mRNA interactions and support the functional division of miRNA structure. Additionally, we present findings related to the localization of transcript target sites, which form the basis for further analyses.
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Affiliation(s)
- Krzysztof Sarapata
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Adrian Kania
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland.
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4
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Iwakawa HO. The clade-specific target recognition mechanisms of plant RISCs. Nucleic Acids Res 2024; 52:6662-6673. [PMID: 38621714 PMCID: PMC11194062 DOI: 10.1093/nar/gkae257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Eukaryotic Argonaut proteins (AGOs) assemble RNA-induced silencing complexes (RISCs) with guide RNAs that allow binding to complementary RNA sequences and subsequent silencing of target genes. The model plant Arabidopsis thaliana encodes 10 different AGOs, categorized into three distinct clades based on amino acid sequence similarity. While clade 1 and 2 RISCs are known for their roles in post-transcriptional gene silencing, and clade 3 RISCs are associated with transcriptional gene silencing in the nucleus, the specific mechanisms of how RISCs from each clade recognize their targets remain unclear. In this study, I conducted quantitative binding analyses between RISCs and target nucleic acids with mismatches at various positions, unveiling distinct target binding characteristics unique to each clade. Clade 1 and 2 RISCs require base pairing not only in the seed region but also in the 3' supplementary region for stable target RNA binding, with clade 1 exhibiting a higher stringency. Conversely, clade 3 RISCs tolerate dinucleotide mismatches beyond the seed region. Strikingly, they bind to DNA targets with an affinity equal to or surpassing that of RNA, like prokaryotic AGO complexes. These insights challenge existing views on plant RNA silencing and open avenues for exploring new functions of eukaryotic AGOs.
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Affiliation(s)
- Hiro-oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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5
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Wang PY, Bartel DP. The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.15.562437. [PMID: 38766062 PMCID: PMC11100590 DOI: 10.1101/2023.10.15.562437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, slicing rates of perfectly complementary, bound targets can be surprisingly different (>250-fold range), and that faster slicing confers better knockdown in cells. Nucleotide sequence identities at guide-RNA positions 7, 10, and 17 underlie much of this variation in slicing rates. Analysis of one of these determinants implicates a structural distortion at guide nucleotides 6-7 in promoting slicing. Moreover, slicing directed by different guide sequences has an unanticipated, 600-fold range in 3'-mismatch tolerance, attributable to guides with weak (AU-rich) central pairing requiring extensive 3' complementarity (pairing beyond position 16) to more fully populate the slicing-competent conformation. Together, our analyses identify sequence determinants of RISC activity and provide biochemical and conformational rationale for their action.
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Affiliation(s)
- Peter Y. Wang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David P. Bartel
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Lead contact
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6
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Brull A, Sarathy A, Bolduc V, Chen GS, McCarty RM, Bönnemann CG. Optimized allele-specific silencing of the dominant-negative COL6A1 G293R substitution causing collagen VI-related dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102178. [PMID: 38617974 PMCID: PMC11015156 DOI: 10.1016/j.omtn.2024.102178] [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: 09/26/2023] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Collagen VI-related dystrophies (COL6-RDs) are a group of severe, congenital-onset muscular dystrophies for which there is no effective causative treatment. Dominant-negative mutations are common in COL6A1, COL6A2, and COL6A3 genes, encoding the collagen α1, α2, and α3 (VI) chains. They act by incorporating into the hierarchical assembly of the three α (VI) chains and consequently produce a dysfunctional collagen VI extracellular matrix, while haploinsufficiency for any of the COL6 genes is not associated with disease. Hence, allele-specific transcript inactivation is a valid therapeutic strategy, although selectively targeting a pathogenic single nucleotide variant is challenging. Here, we develop a small interfering RNA (siRNA) that robustly, and in an allele-specific manner, silences a common glycine substitution (G293R) caused by a single nucleotide change in COL6A1 gene. By intentionally introducing an additional mismatch into the siRNA design, we achieved enhanced specificity toward the mutant allele. Treatment of patient-derived fibroblasts effectively reduced the levels of mutant transcripts while maintaining unaltered wild-type transcript levels, rescuing the secretion and assembly of collagen VI matrix by reducing the dominant-negative effect of mutant chains. Our findings establish a promising treatment approach for patients with the recurrent dominantly negative acting G293R glycine substitution.
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Affiliation(s)
- Astrid Brull
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Apurva Sarathy
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Véronique Bolduc
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grace S. Chen
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Riley M. McCarty
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carsten G. Bönnemann
- Neurogenetics and Neuromuscular Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Todisco M, Ding D, Szostak JW. Transient states during the annealing of mismatched and bulged oligonucleotides. Nucleic Acids Res 2024; 52:2174-2187. [PMID: 38348869 PMCID: PMC10954449 DOI: 10.1093/nar/gkae091] [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: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.
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Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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8
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M. The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res 2024; 52:2530-2545. [PMID: 38197228 PMCID: PMC10954474 DOI: 10.1093/nar/gkad1241] [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: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danielis Rutkauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Evelina Zagorskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvinas Jurgelaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
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9
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Jadhav V, Vaishnaw A, Fitzgerald K, Maier MA. RNA interference in the era of nucleic acid therapeutics. Nat Biotechnol 2024; 42:394-405. [PMID: 38409587 DOI: 10.1038/s41587-023-02105-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/15/2023] [Indexed: 02/28/2024]
Abstract
Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering RNA (siRNA) drug development, including the first approval in 2018 of a liver-targeted siRNA interference (RNAi) therapeutic in lipid nanoparticles and subsequent approvals of five more RNAi drugs, which used metabolically stable siRNAs combined with N-acetylgalactosamine ligands for conjugate-based liver delivery. We also consider the remaining challenges in the field, such as delivery to muscle, brain and other extrahepatic organs. Today's RNAi therapeutics exhibit high specificity, potency and durability, and are transitioning from applications in rare diseases to widespread, chronic conditions.
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Affiliation(s)
- Vasant Jadhav
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Akshay Vaishnaw
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Kevin Fitzgerald
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Martin A Maier
- Research & Development, Alnylam Pharmaceuticals, Cambridge, MA, USA.
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10
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Diener C, Keller A, Meese E. The miRNA-target interactions: An underestimated intricacy. Nucleic Acids Res 2024; 52:1544-1557. [PMID: 38033323 PMCID: PMC10899768 DOI: 10.1093/nar/gkad1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.
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Affiliation(s)
- Caroline Diener
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
| | - Andreas Keller
- Saarland University (USAAR), Chair for Clinical Bioinformatics, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Saarland University (USAAR), Institute of Human Genetics, 66421 Homburg, Germany
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11
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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12
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Chen J, Sheng CW, Peng Y, Wang K, Jiao Y, Palli SR, Cao H. Transcript Level and Sequence Matching Are Key Determinants of Off-Target Effects in RNAi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:577-589. [PMID: 38135672 DOI: 10.1021/acs.jafc.3c07434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Double-stranded RNA (dsRNA) pesticides, those based on RNA interference (RNAi) technology utilizing dsRNA, have shown potential for pest control. However, the off-target effects of dsRNA pose limitations to the widespread application of RNAi and raise concerns regarding potential side effects on other beneficial organisms. The precise impact and underlying factors of these off-target effects are still not well understood. Here, we found that the transcript level and sequence matching jointly regulate off-target effects of dsRNA. The much lower expressed target genes were knocked down to a lesser extent than genes with higher expression levels, and the critical sequence identity of off-target effects is approximately 80%. Moreover, off-target effects could be triggered by a contiguous matching sequence length exceeding 15 nt as well as nearly perfectly matching sequences with one or two base mismatches exceeding 19 nt. Increasing the dosage of dsRNA leads to more severe off-target effects. However, the length of mismatched dsRNA, the choice of different RNAi targets, and the location of target sites within the same gene do not affect the severity of off-target effects. These parameters can be used to guide the design of possibly selective sequences for RNAi, optimize the specificity and efficiency of dsRNA, and facilitate practical applications of RNAi for pest control.
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Affiliation(s)
- Jiasheng Chen
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Cheng-Wang Sheng
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Yingchuan Peng
- Institute of Entomology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kangxu Wang
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210046, China
| | - Yaoyu Jiao
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Haiqun Cao
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
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13
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Monopoli KR, Korkin D, Khvorova A. Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:93-109. [PMID: 37456778 PMCID: PMC10338369 DOI: 10.1016/j.omtn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Chemically modified small interfering RNAs (siRNAs) are promising therapeutics guiding sequence-specific silencing of disease genes. Identifying chemically modified siRNA sequences that effectively silence target genes remains challenging. Such determinations necessitate computational algorithms. Machine learning is a powerful predictive approach for tackling biological problems but typically requires datasets significantly larger than most available siRNA datasets. Here, we describe a framework applying machine learning to a small dataset (356 modified sequences) for siRNA efficacy prediction. To overcome noise and biological limitations in siRNA datasets, we apply a trichotomous, two-threshold, partitioning approach, producing several combinations of classification threshold pairs. We then test the effects of different thresholds on random forest machine learning model performance using a novel evaluation metric accounting for class imbalances. We identify thresholds yielding a model with high predictive power, outperforming a linear model generated from the same data, that was predictive upon experimental evaluation. Using a novel model feature extraction method, we observe target site base importances and base preferences consistent with our current understanding of the siRNA-mediated silencing mechanism, with the random forest providing higher resolution than the linear model. This framework applies to any classification challenge involving small biological datasets, providing an opportunity to develop high-performing design algorithms for oligonucleotide therapies.
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Affiliation(s)
- Kathryn R. Monopoli
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dmitry Korkin
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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14
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Danckwardt S, Trégouët DA, Castoldi E. Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders. Cardiovasc Res 2023; 119:1624-1640. [PMID: 36943786 PMCID: PMC10325701 DOI: 10.1093/cvr/cvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 03/23/2023] Open
Abstract
The haemostatic system is pivotal to maintaining vascular integrity. Multiple components involved in blood coagulation have central functions in inflammation and immunity. A derailed haemostasis is common in prevalent pathologies such as sepsis, cardiovascular disorders, and lately, COVID-19. Physiological mechanisms limit the deleterious consequences of a hyperactivated haemostatic system through adaptive changes in gene expression. While this is mainly regulated at the level of transcription, co- and posttranscriptional mechanisms are increasingly perceived as central hubs governing multiple facets of the haemostatic system. This layer of regulation modulates the biogenesis of haemostatic components, for example in situations of increased turnover and demand. However, they can also be 'hijacked' in disease processes, thereby perpetuating and even causally entertaining associated pathologies. This review summarizes examples and emerging concepts that illustrate the importance of posttranscriptional mechanisms in haemostatic control and crosstalk with the immune system. It also discusses how such regulatory principles can be used to usher in new therapeutic concepts to combat global medical threats such as sepsis or cardiovascular disorders.
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Affiliation(s)
- Sven Danckwardt
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Centre for Cardiovascular Research (DZHK),
Berlin, Germany
- Posttranscriptional Gene Regulation, University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University
Medical Centre Mainz, Langenbeckstr. 1, 55131
Mainz, Germany
- Center for Healthy Aging (CHA), Mainz,
Germany
| | - David-Alexandre Trégouët
- INSERM, Bordeaux Population Health Research Center, UMR 1219, Department of
Molecular Epidemiology of Vascular and Brain Disorders (ELEANOR), University of
Bordeaux, Bordeaux, France
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht
(CARIM), Maastricht University, Universiteitsingel 50, 6229
ER Maastricht, The Netherlands
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15
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Asai T, Yokota M, Isomura H, Koide H, Sakurai N, Okamoto A, Ando H, Dewa T, Oku N. Treatment of PTEN-Null Breast Cancer by a Synthetic Lethal Approach Involving PARP1 Gene Silencing. J Pharm Sci 2023; 112:1908-1914. [PMID: 36828124 DOI: 10.1016/j.xphs.2023.02.017] [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: 01/12/2023] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
The loss of the phosphatase and tensin homolog (PTEN) deleted from chromosome 10 is frequently observed in a variety of human cancers and appears to be an ideal target in synthetic lethality-based treatment. In this study, the synthetic lethal interaction between PTEN loss and the gene silencing of poly [ADP-ribose] polymerase 1 (PARP1) was examined in human triple-negative breast cancer cells (PTEN-null MDA-MB-468 and PTEN-positive MDA-MB-231 cells). Polycation liposomes previously developed by us were employed to deliver the small interfering ribonucleic acid (siRNA) targeted toward PARP1 (siPARP1) into the cancer cells. The silencing of the PARP1 gene exerted a cytocidal effect on the MDA-MB-468 cells but had no effect on the MDA-MB-231 cells and the human umbilical vein endothelial cells employed as normal cells. The simultaneous knockdown of PARP1 and PTEN in the MDA-MB-231 cells resulted in the significant inhibition of cell growth. The data suggest that the effects of the PARP1 knockdown on the cells were dependent on the PTEN status. A significant increase in the DNA breaks and the extent of apoptosis, possibly due to the failure of DNA repair, was observed upon PARP1 knockdown in the MDA-MB-468 cells compared with the case in the MDA-MB-231 cells. Our findings suggest that the synthetic lethal approach via PARP1 gene silencing holds promise for the treatment of patients with PTEN-null breast cancer.
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Affiliation(s)
- Tomohiro Asai
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
| | - Masafumi Yokota
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hideki Isomura
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroyuki Koide
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Naoyuki Sakurai
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Ayaka Okamoto
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; Japan Society for the Promotion of Science (JSPS), 8 Ichibancho, Chiyoda-ku, Tokyo 102-8472, Japan
| | - Hidenori Ando
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Takehisa Dewa
- Department of Life and Materials Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555 Japan
| | - Naoto Oku
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605 Japan
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16
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Lisitskaya L, Kropocheva E, Agapov A, Prostova M, Panteleev V, Yudin D, Ryazansky S, Kuzmenko A, Aravin A, Esyunina D, Kulbachinskiy A. Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo. Nucleic Acids Res 2023; 51:5106-5124. [PMID: 37094066 PMCID: PMC10250240 DOI: 10.1093/nar/gkad290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) and are also thought to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and little is known about their functional activities and target specificities in vivo. Here, we describe five pAgos from mesophilic bacteria that act as programmable DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmids and chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum, can induce DNA interference between homologous sequences resulting in targeted processing of multicopy plasmid and genomic elements. EmaAgo also protects bacteria from bacteriophage infection, by loading phage-derived guide DNAs and decreasing phage DNA content and phage titers. Thus, the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Ekaterina Kropocheva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Maria Prostova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Vladimir Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny141700, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
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17
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Hariharan VN, Caiazzi J, Miller R, Ferguson C, Sapp E, Fakih H, Tang Q, Yamada N, Furgal R, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho B, Hildebrand S, Echeverria D, Hassler M, Alterman J, DiFiglia M, Aronin N, Khvorova A, Yamada K. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. RESEARCH SQUARE 2023:rs.3.rs-2987323. [PMID: 37398145 PMCID: PMC10312934 DOI: 10.21203/rs.3.rs-2987323/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~ 32-fold over PS backbone and > 1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~ 6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
| | | | | | - Chantal Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Qi Tang
- University of Massachusetts Chan Medical School
| | | | | | | | | | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | - Bruno Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School
| | | | | | | | - Neil Aronin
- University of Massachusetts Worcester Campus
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18
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Salama II, Sami SM, Salama SI, Abdel-Latif GA, Shaaban FA, Fouad WA, Abdelmohsen AM, Raslan HM. Current and novel modalities for management of chronic hepatitis B infection. World J Hepatol 2023; 15:585-608. [PMID: 37305370 PMCID: PMC10251278 DOI: 10.4254/wjh.v15.i5.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/13/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over 296 million people are estimated to have chronic hepatitis B viral infection (CHB), and it poses unique challenges for elimination. CHB is the result of hepatitis B virus (HBV)-specific immune tolerance and the presence of covalently closed circular DNA as mini chromosome inside the nucleus and the integrated HBV. Serum hepatitis B core-related antigen is the best surrogate marker for intrahepatic covalently closed circular DNA. Functional HBV “cure” is the durable loss of hepatitis B surface antigen (HBsAg), with or without HBsAg seroconversion and undetectable serum HBV DNA after completing a course of treatment. The currently approved therapies are nucleos(t)ide analogues, interferon-alpha, and pegylated-interferon. With these therapies, functional cure can be achieved in < 10% of CHB patients. Any variation to HBV or the host immune system that disrupts the interaction between them can lead to reactivation of HBV. Novel therapies may allow efficient control of CHB. They include direct acting antivirals and immunomodulators. Reduction of the viral antigen load is a crucial factor for success of immune-based therapies. Immunomodulatory therapy may lead to modulation of the host immune system. It may enhance/restore innate immunity against HBV (as toll-like-receptors and cytosolic retinoic acid inducible gene I agonist). Others may induce adaptive immunity as checkpoint inhibitors, therapeutic HBV vaccines including protein (HBsAg/preS and hepatitis B core antigen), monoclonal or bispecific antibodies and genetically engineered T cells to generate chimeric antigen receptor-T or T-cell receptor-T cells and HBV-specific T cells to restore T cell function to efficiently clear HBV. Combined therapy may successfully overcome immune tolerance and lead to HBV control and cure. Immunotherapeutic approaches carry the risk of overshooting immune responses causing uncontrolled liver damage. The safety of any new curative therapies should be measured in relation to the excellent safety of currently approved nucleos(t)ide analogues. Development of novel antiviral and immune modulatory therapies should be associated with new diagnostic assays used to evaluate the effectiveness or to predict response.
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Affiliation(s)
- Iman Ibrahim Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Samia M Sami
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Somaia I Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Ghada A Abdel-Latif
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Fatma A Shaaban
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Walaa A Fouad
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Aida M Abdelmohsen
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Hala M Raslan
- Department of Internal Medicine, National Research Centre, Giza 12411, Dokki, Egypt
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19
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Yamada K, Hariharan VN, Caiazzi J, Miller R, Furguson C, Sapp E, Fakih H, Tan Q, Yamada N, Furgal RC, Paquette J, Bramato B, McHugh N, Summers A, Lochmann C, Godinho BM, Hildebrand S, Echeverria D, Hassler MR, Alterman JF, DiFiglia M, Aronin N, Khvorova A. Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542506. [PMID: 37292886 PMCID: PMC10245983 DOI: 10.1101/2023.05.26.542506] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3'- and 5'-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3'-exonuclease by ~32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure (~6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Vignesh Narayan Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Chantal Furguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Hassan Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Qi Tan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nozomi Yamada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Raymond C. Furgal
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Joseph Paquette
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Brianna Bramato
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Clemens Lochmann
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew R. Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and Mass General Institute for Neurodegenerative Disease, Charlestown, Massachusetts, United State
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Department of Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, United States
- Program in Molecular Medicine, University of Massachusetts Chan Medical School; Charlestown, Massachusetts, United State
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20
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Xiao Y, Liu TM, MacRae IJ. A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength. EMBO Rep 2023:e55806. [PMID: 37082939 DOI: 10.15252/embr.202255806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/22/2023] Open
Abstract
Argonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) as guides to regulate gene expression in plants and animals. AGOs that use miRNAs in bilaterian animals recognize short (6-8 nt.) elements complementary to the miRNA seed region, enabling each miRNA to interact with hundreds of otherwise unrelated targets. By contrast, AGOs that use miRNAs in plants employ longer (> 13 nt.) recognition elements such that each miRNA silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal AGO proteins: a 9-amino acid loop in the PIWI domain. Swapping the PIWI loop from human Argonaute2 (HsAGO2) into Arabidopsis Argonaute10 (AtAGO10) increases seed strength, resulting in animal-like miRNA targeting. Conversely, swapping the plant PIWI loop into HsAGO2 reduces seed strength and accelerates the turnover of cleaved targets. The loop-swapped HsAGO2 silences targets more potently, with reduced miRNA-like targeting, than wild-type HsAGO2 in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - TingYu M Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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21
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Panteleev V, Kropocheva E, Esyunina D, Kulbachinskiy A. Strong temperature effects on the fidelity of target DNA recognition by a thermophilic pAgo nuclease. Biochimie 2023; 209:142-149. [PMID: 36804511 DOI: 10.1016/j.biochi.2023.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/22/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
Prokaryotic Argonaute (pAgo) proteins are programmable nucleases with great promise in genetic engineering and biotechnology. Previous studies identified several DNA-targeting pAgo nucleases from mesophilic and thermophilic prokaryotic species that are active in various temperature ranges. However, the effects of temperature on the specificity of target recognition and cleavage by pAgos have not been studied. Here, we describe a thermostable pAgo nuclease from the thermophilic bacterium Thermobrachium celere, TceAgo. We show that TceAgo preferentially uses 5'-phosphorylated small DNA guides and can perform specific cleavage of both single-stranded and double-stranded DNA substrates in a wide range of temperatures. Single-nucleotide mismatches between guide and target molecules differently change the reaction efficiency depending on the mismatch position, with the fidelity of target recognition greatly increased at elevated temperatures. Thus, TceAgo can serve as a tool to allow specific detection and cleavage of DNA targets in a temperature-dependent manner. The results demonstrate that the specificity of programmable nucleases can be strongly affected by the reaction conditions, which should be taken into account when using these nucleases in various in vitro and in vivo applications.
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Affiliation(s)
- Vladimir Panteleev
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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22
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Santos D, Feng M, Kolliopoulou A, Taning CNT, Sun J, Swevers L. What Are the Functional Roles of Piwi Proteins and piRNAs in Insects? INSECTS 2023; 14:insects14020187. [PMID: 36835756 PMCID: PMC9962485 DOI: 10.3390/insects14020187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/01/2023]
Abstract
Research on Piwi proteins and piRNAs in insects has focused on three experimental models: oogenesis and spermatogenesis in Drosophila melanogaster, the antiviral response in Aedes mosquitoes and the molecular analysis of primary and secondary piRNA biogenesis in Bombyx mori-derived BmN4 cells. Significant unique and complementary information has been acquired and has led to a greater appreciation of the complexity of piRNA biogenesis and Piwi protein function. Studies performed in other insect species are emerging and promise to add to the current state of the art on the roles of piRNAs and Piwi proteins. Although the primary role of the piRNA pathway is genome defense against transposons, particularly in the germline, recent findings also indicate an expansion of its functions. In this review, an extensive overview is presented of the knowledge of the piRNA pathway that so far has accumulated in insects. Following a presentation of the three major models, data from other insects were also discussed. Finally, the mechanisms for the expansion of the function of the piRNA pathway from transposon control to gene regulation were considered.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
| | - Clauvis N. T. Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
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23
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Roh EH, Sullivan MO, Epps TH. A kinetic modeling platform for predicting the efficacy of siRNA formulations in vitro and in vivo. STAR Protoc 2022; 3:101723. [PMID: 36313537 PMCID: PMC9597118 DOI: 10.1016/j.xpro.2022.101723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present a computational modeling protocol that can accurately predict changes in both in vitro and in vivo gene expression levels in response to the application of various siRNA formulations. We describe how to use this Python-based pipeline to obtain crucial information, namely maximum silencing level and duration of silencing, toward the design of therapeutically relevant dosing regimens. The protocol details the steps for running internalization rate fitting to produce predictions based on experimental measurements from a single time point. For complete details on the use and execution of this protocol, please refer to Roh et al., 2021. Protocol to predict siRNA formulation efficacy using data from a single time point Applicable to various cell types and nanocarriers Translation of in vitro experimental silencing data to predict in vivo results
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Esther H. Roh
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Millicent O. Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA,Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA,Corresponding author
| | - Thomas H. Epps
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA,Center for Research in Soft matter and Polymers (CRiSP), University of Delaware, Newark, DE 19716, USA,Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA,Corresponding author
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24
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Conroy F, Miller R, Alterman JF, Hassler MR, Echeverria D, Godinho BMDC, Knox EG, Sapp E, Sousa J, Yamada K, Mahmood F, Boudi A, Kegel-Gleason K, DiFiglia M, Aronin N, Khvorova A, Pfister EL. Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in Huntington's disease models. Nat Commun 2022; 13:5802. [PMID: 36192390 PMCID: PMC9530163 DOI: 10.1038/s41467-022-33061-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Small interfering RNAs are a new class of drugs, exhibiting sequence-driven, potent, and sustained silencing of gene expression in vivo. We recently demonstrated that siRNA chemical architectures can be optimized to provide efficient delivery to the CNS, enabling development of CNS-targeted therapeutics. Many genetically-defined neurodegenerative disorders are dominant, favoring selective silencing of the mutant allele. In some cases, successfully targeting the mutant allele requires targeting single nucleotide polymorphism (SNP) heterozygosities. Here, we use Huntington’s disease (HD) as a model. The optimized compound exhibits selective silencing of mutant huntingtin protein in patient-derived cells and throughout the HD mouse brain, demonstrating SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. Targeting a disease-causing allele using RNAi-based therapies could be helpful in a range of dominant CNS disorders where maintaining wild-type expression is essential. Chemically modified siRNAs distinguish between mutant and normal huntingtin based on a single nucleotide difference and lower mutant huntingtin specifically in patient derived cells and in a mouse model of Huntington’s disease.
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Affiliation(s)
- Faith Conroy
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Rachael Miller
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Emily G Knox
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaquelyn Sousa
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Ken Yamada
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Farah Mahmood
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Kimberly Kegel-Gleason
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Neil Aronin
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA.,RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, 01605, USA.
| | - Edith L Pfister
- Department of Medicine, UMass Chan Medical School, Worcester, MA, 01605, USA.
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25
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Arif A, Bailey S, Izumi N, Anzelon TA, Ozata DM, Andersson C, Gainetdinov I, MacRae IJ, Tomari Y, Zamore PD. GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature 2022; 608:618-625. [PMID: 35772669 PMCID: PMC9385479 DOI: 10.1038/s41586-022-05009-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
Argonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins have diverse biological functions and many retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, the PIWI proteins-a specialized class of Argonaute proteins-use 21-35 nucleotide PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalysed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2) and MIWI22-4 (PIWIL4). The piRNA-guided endoribonuclease activities of MIWI and MILI are essential for the production of functional sperm5,6. piRNA-directed silencing in mice and insects also requires GTSF1, a PIWI-associated protein of unknown function7-12. Here we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 is thus an example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
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Affiliation(s)
- Amena Arif
- Department of Biochemistry and Molecular Biotechnology Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Beam Therapeutics, Cambridge, MA, USA
| | - Shannon Bailey
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Natsuko Izumi
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Todd A Anzelon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Deniz M Ozata
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Cecilia Andersson
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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26
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Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2. Nat Commun 2022; 13:3825. [PMID: 35780145 PMCID: PMC9250533 DOI: 10.1038/s41467-022-31480-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
Human Argonaute 2 (hAgo2) constitutes the functional core of the RNA interference pathway. Guide RNAs direct hAgo2 to target mRNAs, which ultimately leads to hAgo2-mediated mRNA degradation or translational inhibition. Here, we combine site-specifically labeled hAgo2 with time-resolved single-molecule FRET measurements to monitor conformational states and dynamics of hAgo2 and hAgo2-RNA complexes in solution that remained elusive so far. We observe dynamic anchoring and release of the guide’s 3’-end from the PAZ domain during the stepwise target loading process even with a fully complementary target. We find differences in structure and dynamic behavior between partially and fully paired canonical hAgo2-guide/target complexes and the miRNA processing complex formed by hAgo2 and pre-miRNA451. Furthermore, we detect a hitherto unknown conformation of hAgo2-guide/target complexes that poises them for target-directed miRNA degradation. Taken together, our results show how the conformational flexibility of hAgo2-RNA complexes determines function and the fate of the ribonucleoprotein particle. Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
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27
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Integrative Analysis of miRNAs and Their Targets Involved in Ray Floret Growth in Gerbera hybrida. Int J Mol Sci 2022; 23:ijms23137296. [PMID: 35806310 PMCID: PMC9266715 DOI: 10.3390/ijms23137296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in regulating many aspects of plant growth and development at the post-transcriptional level. Gerbera (Gerbera hybrida) is an important ornamental crop. However, the role of miRNAs in the growth and development of gerbera is still unclear. In this study, we used high-throughput sequencing to analyze the expression profiles of miRNAs in ray floret during inflorescence opening. A total of 164 miRNAs were obtained, comprising 24 conserved miRNAs and 140 novel miRNAs. Ten conserved and 15 novel miRNAs were differentially expressed during ray floret growth, and 607 differentially expressed target genes of these differentially expressed miRNAs were identified using psRNATarget. We performed a comprehensive analysis of the expression profiles of the miRNAs and their targets. The changes in expression of five miRNAs (ghy-miR156, ghy-miR164, ghy-miRn24, ghy-miRn75 and ghy-miRn133) were inversely correlated with the changes in expression of their eight target genes. The miRNA cleavage sites in candidate target gene mRNAs were determined using 5′-RLM-RACE. Several miRNA-mRNA pairs were predicted to regulate ray floret growth and anthocyanin biosynthesis. In conclusion, the results of small RNA sequencing provide valuable information to reveal the mechanisms of miRNA-mediated ray floret growth and anthocyanin accumulation in gerbera.
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28
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Akbar S, Wei Y, Zhang MQ. RNA Interference: Promising Approach to Combat Plant Viruses. Int J Mol Sci 2022; 23:ijms23105312. [PMID: 35628126 PMCID: PMC9142109 DOI: 10.3390/ijms23105312] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022] Open
Abstract
Plant viruses are devastating plant pathogens that severely affect crop yield and quality. Plants have developed multiple lines of defense systems to combat viral infection. Gene silencing/RNA interference is the key defense system in plants that inhibits the virulence and multiplication of pathogens. The general mechanism of RNAi involves (i) the transcription and cleavage of dsRNA into small RNA molecules, such as microRNA (miRNA), or small interfering RNA (siRNA), (ii) the loading of siRNA/miRNA into an RNA Induced Silencing Complex (RISC), (iii) complementary base pairing between siRNA/miRNA with a targeted gene, and (iv) the cleavage or repression of a target gene with an Argonaute (AGO) protein. This natural RNAi pathway could introduce transgenes targeting various viral genes to induce gene silencing. Different RNAi pathways are reported for the artificial silencing of viral genes. These include Host-Induced Gene Silencing (HIGS), Virus-Induced Gene Silencing (VIGS), and Spray-Induced Gene Silencing (SIGS). There are significant limitations in HIGS and VIGS technology, such as lengthy and time-consuming processes, off-target effects, and public concerns regarding genetically modified (GM) transgenic plants. Here, we provide in-depth knowledge regarding SIGS, which efficiently provides RNAi resistance development against targeted genes without the need for GM transgenic plants. We give an overview of the defense system of plants against viral infection, including a detailed mechanism of RNAi, small RNA molecules and their types, and various kinds of RNAi pathways. This review will describe how RNA interference provides the antiviral defense, recent improvements, and their limitations.
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Affiliation(s)
- Sehrish Akbar
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
| | - Yao Wei
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
| | - Mu-Qing Zhang
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA
- Correspondence: or
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29
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Li W, Liu Y, He R, Wang L, Wang Y, Zeng W, Zhang Z, Wang F, Ma L. A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis. Nucleic Acids Res 2022; 50:5226-5238. [PMID: 35524569 PMCID: PMC9122594 DOI: 10.1093/nar/gkac315] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Argonaute (Ago) proteins are programmable nucleases found in eukaryotes and prokaryotes. Prokaryotic Agos (pAgos) share a high degree of structural homology with eukaryotic Agos (eAgos), and eAgos originate from pAgos. Although eAgos exclusively cleave RNA targets, most characterized pAgos cleave DNA targets. This study characterized a novel pAgo, MbpAgo, from the psychrotolerant bacterium Mucilaginibacter paludis which prefers to cleave RNA targets rather than DNA targets. Compared to previously studied Agos, MbpAgo can utilize both 5′phosphorylated(5′P) and 5′hydroxylated(5′OH) DNA guides (gDNAs) to efficiently cleave RNA targets at the canonical cleavage site if the guide is between 15 and 17 nt long. Furthermore, MbpAgo is active at a wide range of temperatures (4–65°C) and displays no obvious preference for the 5′-nucleotide of a guide. Single-nucleotide and most dinucleotide mismatches have no or little effects on cleavage efficiency, except for dinucleotide mismatches at positions 11–13 that dramatically reduce target cleavage. MbpAgo can efficiently cleave highly structured RNA targets using both 5′P and 5′OH gDNAs in the presence of Mg2+ or Mn2+. The biochemical characterization of MbpAgo paves the way for its use in RNA manipulations such as nucleic acid detection and clearance of RNA viruses.
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Affiliation(s)
- Wenqiang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ruyi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanting Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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30
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Characterization of a Programmable Argonaute Nuclease from the Mesophilic Bacterium Rummeliibacillus suwonensis. Biomolecules 2022; 12:biom12030355. [PMID: 35327547 PMCID: PMC8945025 DOI: 10.3390/biom12030355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/08/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022] Open
Abstract
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from Kurthia massiliensis can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from Rummeliibacillus suwonensis is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16–20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5′-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
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31
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Hui RWH, Mak LY, Seto WK, Yuen MF. RNA interference as a novel treatment strategy for chronic hepatitis B infection. Clin Mol Hepatol 2022; 28:408-424. [PMID: 35172540 PMCID: PMC9293617 DOI: 10.3350/cmh.2022.0012] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Chronic hepatitis B (CHB) is a major cause of liver-related morbidity and mortality. Functional cure of CHB, defined as sustainable hepatitis B surface antigen (HBsAg) seroclearance, is associated with improved clinical outcomes. However, functional cure is rarely attainable by current treatment modalities. RNA interference (RNAi) by small-interfering RNA (siRNA) and anti-sense oligonucleotide (ASO) has been studied as a novel treatment strategy for CHB. RNAi targets post-transcriptional messenger RNAs and pregenomic RNAs to reduce hepatitis B virus (HBV) antigen production and viral replication. By reducing viral antigens, host immune reconstitution against HBV may also be attained. Phase I/II trials on siRNAs have demonstrated them to be safe and well-tolerated. siRNA is effective when given in monthly doses with different total number of doses according to different trial design, and can lead to sustainable dose-dependent mean HBsAg reduction by 2–2.5 log. Incidences of HBsAg seroclearance after siRNA therapy have also been reported. ASOs have also been studied in early phase trials, and a phase Ib study using frequent dosing regimen within 4 weeks could achieve similar HBsAg reduction of 2 log from baseline. Given the established efficacy and safety of nucleos(t) ide analogues (NAs), future RNAi regimens will likely include NA backbone. While the current evidence on RNAi appears promising, it remains undetermined whether the potent HBsAg reduction by RNAi can result in a high rate of HBsAg seroclearance with durability. Data on RNAi from phase IIb/III trials are keenly anticipated.
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Affiliation(s)
- Rex Wan-Hin Hui
- Department of Medicine, The University of Hong Kong, Hong Kong
| | - Lung-Yi Mak
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Wai-Kay Seto
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
| | - Man-Fung Yuen
- Department of Medicine, The University of Hong Kong, Hong Kong.,State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong
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32
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Iwakawa HO, Tomari Y. Life of RISC: Formation, action, and degradation of RNA-induced silencing complex. Mol Cell 2021; 82:30-43. [PMID: 34942118 DOI: 10.1016/j.molcel.2021.11.026] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023]
Abstract
Small RNAs regulate a wide variety of biological processes by repressing the expression of target genes at the transcriptional and post-transcriptional levels. To achieve these functions, small RNAs form RNA-induced silencing complex (RISC) together with a member of the Argonaute (AGO) protein family. RISC is directed by its bound small RNA to target complementary RNAs and represses their expression through mRNA cleavage, degradation, and/or translational repression. Many different factors fine-tune RISC activity and stability-from guide-target RNA complementarity to the recruitment of other protein partners to post-translational modifications of RISC itself. Here, we review recent progress in understanding RISC formation, action, and degradation, and discuss new, intriguing questions in the field.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
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33
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Martin MD, Brown DN, Ramos KS. Computational modeling of RNase, antisense ORF0 RNA, and intracellular compartmentation and their impact on the life cycle of the line retrotransposon. Comput Struct Biotechnol J 2021; 19:5667-5677. [PMID: 34765087 PMCID: PMC8554170 DOI: 10.1016/j.csbj.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 11/08/2022] Open
Abstract
Nearly half of the human genome is occupied by repetitive sequences of ancient virus-like genetic elements. The largest class, comprising 17% of the genome, belong to the type 1 Long INterspersed Elements (LINE-1) and are the only class capable of autonomous propagation in the genome. When epigenetic silencing mechanisms of LINE-1 fail, the proteins encoded by LINE-1 engage in reverse transcription to make new copies of their own or other DNAs that are pasted back into the genome. To elucidate how LINE-1 is dysregulated as a result of carcinogen exposure, we developed a computational model of key elements in the LINE-1 lifecycle, namely, the role of cytosolic ribonuclease (RNase), RNA interference (RNAi) by the antisense ORF0 RNA, and sequestration of LINE-1 products into stress granules and multivesicular structures. The model showed that when carcinogen exposure is represented as either a sudden increase in LINE-1 mRNA count, or as an increase in mRNA transcription rate, the retrotransposon copy number exhibits a distinct threshold behavior above which LINE-1 enters a positive feedback loop that allows the cDNA copy number to grow exponentially. We also found that most of the LINE-1 RNA was degraded via the RNAase pathway and that neither ORF0 RNAi, nor the sequestration of LINE-1 products into granules and multivesicular structures, played a significant role in regulating the retrotransposon’s life cycle. Several aspects of the prediction agree with experimental results and indicate that the model has significant potential to inform future experiments related to LINE-1 activation.
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Affiliation(s)
| | - David N Brown
- Western Kentucky University, 1906 College Heights Blvd, Bowling Green, Kentucky 42101, United States
| | - Kenneth S Ramos
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, United States
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34
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Roh E, Epps TH, Sullivan MO. Kinetic Modeling to Accelerate the Development of Nucleic Acid Formulations. ACS NANO 2021; 15:16055-16066. [PMID: 34636541 PMCID: PMC8860063 DOI: 10.1021/acsnano.1c04555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A critical hurdle in the clinical translation of nucleic acid drugs is the inefficiency in testing formulations for therapeutic potential. Specifically, the ability to quantitatively predict gene expression is lacking when transitioning between cell culture and animal studies. We address this challenge by developing a mathematical framework that can reliably predict short-interfering RNA (siRNA)-mediated gene silencing with as few as one experimental data point as an input, evaluate the efficacies of existing formulations in an expeditious manner, and ultimately guide the design of nanocarriers with optimized performances. The model herein consisted of only essential rate-limiting steps and parameters with easily characterizable values of the RNA interference process, enabling the easy identification of which parameters play dominant roles in determining the potencies of siRNA formulations. Predictions from our framework were in close agreement with in vitro and in vivo experimental results across a retrospective analysis using multiple published data sets. Notably, our findings suggested that siRNA dilution was the primary determinant of gene-silencing kinetics. Our framework shed light on the fact that this dilution rate is governed by different parameters, i.e., cell dilution (in vitro) versus clearance from target tissue (in vivo), highlighting a key reason why in vitro experiments do not always predict in vivo outcomes. Moreover, although our current effort focuses on siRNA, we anticipate that the framework can be modified and applied to other nucleic acids, such as mRNA, that rely on similar biological processes.
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Affiliation(s)
- Esther
H. Roh
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Thomas H. Epps
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Center
for Research in Soft matter and Polymers (CRiSP), University of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United
States
| | - Millicent O. Sullivan
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department
of Biomedical Engineering, University of
Delaware, Newark, Delaware 19716, United
States
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35
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Rozen-Gagnon K, Gu M, Luna JM, Luo JD, Yi S, Novack S, Jacobson E, Wang W, Paul MR, Scheel TKH, Carroll T, Rice CM. Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. Cell Host Microbe 2021; 29:834-848.e13. [PMID: 33794184 DOI: 10.1016/j.chom.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Argonaute (AGO) proteins bind small RNAs to silence complementary RNA transcripts, and they are central to RNA interference (RNAi). RNAi is critical for regulation of gene expression and antiviral defense in Aedes aegypti mosquitoes, which transmit Zika, chikungunya, dengue, and yellow fever viruses. In mosquitoes, AGO1 mediates miRNA interactions, while AGO2 mediates siRNA interactions. We applied AGO-crosslinking immunoprecipitation (AGO-CLIP) for both AGO1 and AGO2, and we developed a universal software package for CLIP analysis (CLIPflexR), identifying 230 small RNAs and 5,447 small RNA targets that comprise a comprehensive RNAi network map in mosquitoes. RNAi network maps predicted expression levels of small RNA targets in specific tissues. Additionally, this resource identified unexpected, context-dependent AGO2 target preferences, including endogenous viral elements and 3'UTRs. Finally, contrary to current thinking, mosquito AGO2 repressed imperfect targets. These findings expand our understanding of small RNA networks and have broad implications for the study of antiviral RNAi.
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Affiliation(s)
- Kathryn Rozen-Gagnon
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
| | - Meigang Gu
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Soon Yi
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Sasha Novack
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Eliana Jacobson
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Wei Wang
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Troels K H Scheel
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Thomas Carroll
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
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36
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Physiologically based pharmacokinetic (PBPK) modeling of RNAi therapeutics: Opportunities and challenges. Biochem Pharmacol 2021; 189:114468. [PMID: 33577889 DOI: 10.1016/j.bcp.2021.114468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
Physiologically based pharmacokinetic (PBPK) modeling is a powerful tool with many demonstrated applications in various phases of drug development and regulatory review. RNA interference (RNAi)-based therapeutics are a class of drugs that have unique pharmacokinetic properties and mechanisms of action. With an increasing number of RNAi therapeutics in the pipeline and reaching the market, there is a considerable amount of active research in this area requiring a multidisciplinary approach. The application of PBPK models for RNAi therapeutics is in its infancy and its utility to facilitate the development of this new class of drugs is yet to be fully evaluated. From this perspective, we briefly discuss some of the current computational modeling approaches used in support of efficient development and approval of RNAi therapeutics. Considerations for PBPK model development are highlighted both in a relative context between small molecules and large molecules such as monoclonal antibodies and as it applies to RNAi therapeutics. In addition, the prospects for drawing upon other recognized avenues of PBPK modeling and some of the foreseeable challenges in PBPK model development for these chemical modalities are briefly discussed. Finally, an exploration of the potential application of PBPK model development for RNAi therapeutics is provided. We hope these preliminary thoughts will help initiate a dialogue between scientists in the relevant sectors to examine the value of PBPK modeling for RNAi therapeutics. Such evaluations could help standardize the practice in the future and support appropriate guidance development for strengthening the RNAi therapeutics development program.
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37
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A novel rationale for targeting FXI: Insights from the hemostatic microRNA targetome for emerging anticoagulant strategies. Pharmacol Ther 2021; 218:107676. [DOI: 10.1016/j.pharmthera.2020.107676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
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38
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Chen J, Peng Y, Zhang H, Wang K, Zhao C, Zhu G, Reddy Palli S, Han Z. Off-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA. RNA Biol 2021; 18:1747-1759. [PMID: 33397184 DOI: 10.1080/15476286.2020.1868680] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RNAi is a potent technique for the knockdown of target genes. However, its potential off-target effects limit the widespread applications in both reverse genetic analysis and genetic manipulation. Previous efforts have uncovered rules underlying specificity of siRNA-based silencing, which has broad applications in humans, but the basis for specificity of dsRNAs, which are better suited for use as insecticides, is poorly understood. Here, we investigated the rules governing dsRNA specificity. Mutational analyses showed that dsRNAs with >80% sequence identity with target genes triggered RNAi efficiently. dsRNAs with ≥16 bp segments of perfectly matched sequence or >26 bp segments of almost perfectly matched sequence with one or two mismatches scarcely distributed (single mismatches inserted between ≥5 bp matching segments or mismatched couplets inserted between ≥8 bp matching segments) also able to trigger RNAi. Using these parameters to predict off-target risk, dsRNAs can be designed to optimize specificity and efficiency, paving the way to the widespread, rational application of RNAi in pest control.
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Affiliation(s)
- Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yingchuan Peng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Institute of Entomology, Jiangxi Agricultural University, Nanchang, China
| | - Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Kangxu Wang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, China
| | - Chunqing Zhao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guanheng Zhu
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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39
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Supe S, Upadhya A, Singh K. Role of small interfering RNA (siRNA) in targeting ocular neovascularization: A review. Exp Eye Res 2020; 202:108329. [PMID: 33198953 DOI: 10.1016/j.exer.2020.108329] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Ocular neovascularization (NV) plays a central role in the pathogenesis of various ocular diseases including diabetic retinopathy, age-related macular degeneration, retinoblastoma, retinitis pigmentosa and may lead to loss of vision if not controlled in time. Several clinical trials elucidate the central role of vascular endothelial growth factor (VEGF) in the pathogenesis of the ocular neovascularization. The advent and extensive use of ocular anti-VEGF therapy heralded a new age in the treatment of retinal vascular and exudative diseases. RNA interference (RNAi) can be used to inhibit the in-vitro and in-vivo expression of specific genes and thus provides an extremely useful method for investigating gene activity with minimal toxicity. siRNA targeting VEGF overcomes many drawbacks associated with the conventional treatment available for the treatment of ocular neovascularization. However, delivery methods that protect the siRNA against degradation and are appropriate for long-term care will help increase the effectiveness of RNAi-based anti-VEGF ocular therapies. Several nanotechnology approaches have been explored by formulation scientists for delivery of siRNA to the eye; targeting particularly VEGF for the treatment of NV. This review mainly focuses on current updates in various pre-clinical and clinical siRNA strategies for targeting VEGF involved in the development of ocular neovascularization.
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Affiliation(s)
- Shibani Supe
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai, 400056, Maharashtra, India
| | - Archana Upadhya
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai, 400056, Maharashtra, India
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai, 400056, Maharashtra, India.
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40
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Medley JC, Panzade G, Zinovyeva AY. microRNA strand selection: Unwinding the rules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1627. [PMID: 32954644 PMCID: PMC8047885 DOI: 10.1002/wrna.1627] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
microRNAs (miRNAs) play a central role in the regulation of gene expression by targeting specific mRNAs for degradation or translational repression. Each miRNA is post‐transcriptionally processed into a duplex comprising two strands. One of the two miRNA strands is selectively loaded into an Argonaute protein to form the miRNA‐Induced Silencing Complex (miRISC) in a process referred to as miRNA strand selection. The other strand is ejected from the complex and is subject to degradation. The target gene specificity of miRISC is determined by sequence complementarity between the Argonaute‐loaded miRNA strand and target mRNA. Each strand of the miRNA duplex has the capacity to be loaded into miRISC and possesses a unique seed sequence. Therefore, miRNA strand selection plays a defining role in dictating the specificity of miRISC toward its targets and provides a mechanism to alter gene expression in a switch‐like fashion. Aberrant strand selection can lead to altered gene regulation by miRISC and is observed in several human diseases including cancer. Previous and emerging data shape the rules governing miRNA strand selection and shed light on how these rules can be circumvented in various physiological and pathological contexts. This article is categorized under:RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
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Affiliation(s)
- Jeffrey C Medley
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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41
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Getz MA, Weinberg DE, Drinnenberg IA, Fink GR, Bartel DP. Xrn1p acts at multiple steps in the budding-yeast RNAi pathway to enhance the efficiency of silencing. Nucleic Acids Res 2020; 48:7404-7420. [PMID: 32501509 PMCID: PMC7528652 DOI: 10.1093/nar/gkaa468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/21/2020] [Accepted: 05/20/2020] [Indexed: 01/12/2023] Open
Abstract
RNA interference (RNAi) is a gene-silencing pathway that can play roles in viral defense, transposon silencing, heterochromatin formation and post-transcriptional gene silencing. Although absent from Saccharomyces cerevisiae, RNAi is present in other budding-yeast species, including Naumovozyma castellii, which have an unusual Dicer and a conventional Argonaute that are both required for gene silencing. To identify other factors that act in the budding-yeast pathway, we performed an unbiased genetic selection. This selection identified Xrn1p, the cytoplasmic 5'-to-3' exoribonuclease, as a cofactor of RNAi in budding yeast. Deletion of XRN1 impaired gene silencing in N. castellii, and this impaired silencing was attributable to multiple functions of Xrn1p, including affecting the composition of siRNA species in the cell, influencing the efficiency of siRNA loading into Argonaute, degradation of cleaved passenger strand and degradation of sliced target RNA.
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Affiliation(s)
- Matthew A Getz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
| | - David E Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
| | - Ines A Drinnenberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
| | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA 02142, USA
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42
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Avendaño-Vázquez SE, Flores-Jasso CF. Stumbling on elusive cargo: how isomiRs challenge microRNA detection and quantification, the case of extracellular vesicles. J Extracell Vesicles 2020; 9:1784617. [PMID: 32944171 PMCID: PMC7480573 DOI: 10.1080/20013078.2020.1784617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- S Eréndira Avendaño-Vázquez
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
| | - C Fabián Flores-Jasso
- Consorcio de Metabolismo de RNA y Vesículas Extracelulares, Instituto Nacional de Medicina Genómica, INMEGEN, Ciudad de México, México
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43
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Genome Editing of the SNAI1 Gene in Rhabdomyosarcoma: A Novel Model for Studies of Its Role. Cells 2020; 9:cells9051095. [PMID: 32354171 PMCID: PMC7290443 DOI: 10.3390/cells9051095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Genome editing (GE) tools and RNA interference technology enable the modulation of gene expression in cancer research. While GE mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 or transcription activator-like effector nucleases (TALEN) activity can be used to induce gene knockouts, shRNA interacts with the targeted transcript, resulting in gene knockdown. Here, we compare three different methods for SNAI1 knockout or knockdown in rhabdomyosarcoma (RMS) cells. RMS is the most common sarcoma in children and its development has been previously associated with SNAI1 transcription factor activity. To investigate the role of SNAI1 in RMS development, we compared CRISPR/Cas9, TALEN, and shRNA tools to identify the most efficient tool for the modulation of SNAI1 expression with biological effects. Subsequently, the genome sequence, transcript levels, and protein expression of SNAI1 were evaluated. The modulation of SNAI1 using three different approaches affected the morphology of the cells and modulated the expression of myogenic factors and HDAC1. Our study revealed a similar effectiveness of the tested methods. Nevertheless, the low efficiency of the GE tools was a limiting factor in obtaining biallelic gene knockouts. To conclude, we established and characterized three different models of SNAI1 knockout and knockdown that might be used in further studies investigating the role of SNAI1 in RMS.
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44
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Svoboda P. Key Mechanistic Principles and Considerations Concerning RNA Interference. FRONTIERS IN PLANT SCIENCE 2020; 11:1237. [PMID: 32903622 PMCID: PMC7438612 DOI: 10.3389/fpls.2020.01237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 07/28/2020] [Indexed: 05/03/2023]
Abstract
Canonical RNAi, one of the so-called RNA-silencing mechanisms, is defined as sequence-specific RNA degradation induced by long double-stranded RNA (dsRNA). RNAi occurs in four basic steps: (i) processing of long dsRNA by RNase III Dicer into small interfering RNA (siRNA) duplexes, (ii) loading of one of the siRNA strands on an Argonaute protein possessing endonucleolytic activity, (iii) target recognition through siRNA basepairing, and (iv) cleavage of the target by the Argonaute's endonucleolytic activity. This basic pathway diversified and blended with other RNA silencing pathways employing small RNAs. In some organisms, RNAi is extended by an amplification loop employing an RNA-dependent RNA polymerase, which generates secondary siRNAs from targets of primary siRNAs. Given the high specificity of RNAi and its presence in invertebrates, it offers an opportunity for highly selective pest control. The aim of this text is to provide an introductory overview of key mechanistic aspects of RNA interference for understanding its potential and constraints for its use in pest control.
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45
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Kuzmenko A, Yudin D, Ryazansky S, Kulbachinskiy A, Aravin AA. Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea. Nucleic Acids Res 2019; 47:5822-5836. [PMID: 31114878 PMCID: PMC6582412 DOI: 10.1093/nar/gkz379] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
Argonaute (Ago) proteins are key players in RNA interference in eukaryotes, where they function as RNA-guided RNA endonucleases. Prokaryotic Argonautes (pAgos) are much more diverse than their eukaryotic counterparts but their cellular functions and mechanisms of action remain largely unknown. Some pAgos were shown to use small DNA guides for endonucleolytic cleavage of complementary DNA in vitro. However, previously studied pAgos from thermophilic prokaryotes function at elevated temperatures, which limits their potential use as a tool in genomic applications. Here, we describe two pAgos from mesophilic bacteria, Clostridium butyricum (CbAgo) and Limnothrix rosea (LrAgo), that act as DNA-guided DNA nucleases at physiological temperatures. In comparison with previously studied pAgos, CbAgo and LrAgo do not show strong preferences for the 5′-nucleotide in guide DNA and can use not only 5′-phosphorylated but also 5′-hydroxyl DNA guides. Both CbAgo and LrAgo can tolerate guide/target mismatches in the seed region, but are sensitive to mismatches in the 3′-guide region. Both pAgos can perform programmable endonucleolytic cleavage of double-stranded DNA substrates, showing enhanced activity at AT-rich regions and at elevated temperatures. The biochemical characterization of mesophilic pAgo proteins paves the way for their use for DNA manipulations both in vitro and in vivo.
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Affiliation(s)
- Anton Kuzmenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Department of Molecular Biology, Biological Faculty, Moscow State University, Moscow 119991, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Department of Molecular Biology, Biological Faculty, Moscow State University, Moscow 119991, Russia
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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46
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Sun Y, Zhang Y, Zhang X. Synonymous SNPs of viral genes facilitate virus to escape host antiviral RNAi immunity. RNA Biol 2019; 16:1697-1710. [PMID: 31416386 DOI: 10.1080/15476286.2019.1656026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Synonymous single nucleotide polymorphisms (SNPs) are involved in codon usage preference or mRNA splicing. Up to date, however, the role of synonymous SNPs in immunity remains unclear. To address this issue, the SNPs of white spot syndrome virus (WSSV) were characterized in shrimp in the present study. Our results indicated that there existed synonymous SNPs in the mRNAs of wsv151 and wsv226, two viral genes of WSSV. In the presence of SNP siRNA, wild-type siRNA, wild-type mRNA and SNP mRNA of wsv151 or wsv226, RNAi was significantly suppressed, showing that the synonymous SNPs of wsv151 and wsv226 played negative roles in host siRNA pathway due to mismatch of siRNA with its target. In insect cells, the mismatch, caused by synonymous SNPs of wsv151 or wsv226, between siRNA and its target inhibited the host RNAi. Furthermore, the data revealed that the co-injection of SNP siRNA and wild-type siRNA of wsv151 or wsv226 into WSSV-infected shrimp led to a significant increase of WSSV copies compared with that of SNP siRNA alone or wild-type siRNA alone, indicating that the synonymous SNPs of viral genes could be a strategy of virus escaping host siRNA pathway in shrimp in vivo. Therefore, our study provided novel insights into the underlying mechanism of virus escaping host antiviral RNAi immunity by synonymous SNPs of viral genes.
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Affiliation(s)
- Yuechao Sun
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yu Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences and Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
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47
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Becker WR, Ober-Reynolds B, Jouravleva K, Jolly SM, Zamore PD, Greenleaf WJ. High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2. Mol Cell 2019; 75:741-755.e11. [PMID: 31324449 PMCID: PMC6823844 DOI: 10.1016/j.molcel.2019.06.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/23/2019] [Accepted: 06/07/2019] [Indexed: 11/16/2022]
Abstract
Argonaute proteins loaded with microRNAs (miRNAs) or small interfering RNAs (siRNAs) form the RNA-induced silencing complex (RISC), which represses target RNA expression. Predicting the biological targets, specificity, and efficiency of both miRNAs and siRNAs has been hamstrung by an incomplete understanding of the sequence determinants of RISC binding and cleavage. We applied high-throughput methods to measure the association kinetics, equilibrium binding energies, and single-turnover cleavage rates of mouse AGO2 RISC. We find that RISC readily tolerates insertions of up to 7 nt in its target opposite the central region of the guide. Our data uncover specific guide:target mismatches that enhance the rate of target cleavage, suggesting novel siRNA design strategies. Using these data, we derive quantitative models for RISC binding and target cleavage and show that our in vitro measurements and models predict knockdown in an engineered cellular system.
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Affiliation(s)
- Winston R Becker
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | | | - Karina Jouravleva
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samson M Jolly
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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Krzysztoń R, Woschée D, Reiser A, Schwake G, Strey HH, Rädler JO. Single-cell kinetics of siRNA-mediated mRNA degradation. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 21:102077. [PMID: 31400572 DOI: 10.1016/j.nano.2019.102077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/26/2022]
Abstract
RNA interference (RNAi) enables the therapeutic use of small interfering RNAs (siRNAs) to silence disease-related genes. The efficiency of silencing is commonly assessed by measuring expression levels of the target protein at a given time point post-transfection. Here, we determine the siRNA-induced fold change in mRNA degradation kinetics from single-cell fluorescence time-courses obtained using live-cell imaging on single-cell arrays (LISCA). After simultaneous transfection of mRNAs encoding eGFP (target) and CayRFP (reference), the eGFP expression is silenced by siRNA. The single-cell time-courses are fitted using a mathematical model of gene expression. Analysis yields best estimates of related kinetic rate constants, including mRNA degradation constants. We determine the siRNA-induced changes in kinetic rates and their correlations between target and reference protein expression. Assessment of mRNA degradation constants using single-cell time-lapse imaging is fast (<30 h) and returns an accurate, time-independent measure of siRNA-induced silencing, thus allowing the exact evaluation of siRNA therapeutics.
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Affiliation(s)
- Rafał Krzysztoń
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany.
| | - Daniel Woschée
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany
| | - Anita Reiser
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany
| | - Gerlinde Schwake
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany
| | - Helmut H Strey
- Department of Biomedical Engineering and Laufer Center for Quantitative Biology, Stony Brook University, Stony Brook, NY
| | - Joachim O Rädler
- Faculty of Physics, Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität Munich (LMU), Munich, Germany; Nano systems Initiative Munich (NIM) and Center for NanoScience (CeNS), Munich, Germany.
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49
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Huerta-Zavala ML, Lopez-Castillejos ES, Requenez-Contreras JL, Granados-Riveron JT, Aquino-Jarquin G. A single miRNA and miRNA sponge expression system for efficient modulation of miR-223 availability in mammalian cells. J Gene Med 2019; 21:e3100. [PMID: 31166636 DOI: 10.1002/jgm.3100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Hundreds of microRNAs (miRNAs), comprising small non-coding RNAs of 20-24 nucleotides, have been discovered, although the entirety of their biological functions is poorly understood. Overexpression or suppression approaches are commonly performed to investigate the function of specific miRNAs. In the present study, we focused on generating a lentiviral vector-based strategy that enables hsa-miR-223-3p (miR-223) overexpression and suppression in the target cells for functional analysis of this miRNA easily and rapidly. METHODS The sequence that gives rise to miR-223 and the sequence generating the sponge RNA with four binding sites for miR-223 were cloned in pLVX-shRNA2 vector. The functionality of the vector to overexpress miR-223 was evaluated by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays, whereas the post-transcriptional regulation exerted by miR-223 was evaluated by luciferase reporter assays in AD-293 cells. The anti-miR-223 sponge activity with one binding site for miR-223 (pmCherry-anti-miR-223) was confirmed by qRT-PCR and the restoration of its target (IKKα) was evaluated by western blot assays in Jurkat cells. RESULTS The pLVX-miR-223 vector is functional for over-expressing miR-223 and regulates the mRNA of MDR1/ABCB1 at the post-transcriptional level in AD-293 cells. The anti-miR-223 sponge with one miR-223 binding site efficiently modulates the miR-223 availability and not the one with four sites. The over-expression of anti-miR-223 correlated with a decrease in the levels of miR-223 and, consequently, with an increase in the expression level of the IKKα protein in Jurkat cells. CONCLUSIONS This single miRNA and miRNA sponge expression system specifically alters the availability of miR-223 in mammalian cells.
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Affiliation(s)
- Mariel Lizbeth Huerta-Zavala
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Erika Sicahui Lopez-Castillejos
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - José Luis Requenez-Contreras
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Javier Tadeo Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
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50
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Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 2019; 20:89-108. [PMID: 30446728 DOI: 10.1038/s41576-018-0073-3] [Citation(s) in RCA: 646] [Impact Index Per Article: 129.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.
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Affiliation(s)
- Deniz M Ozata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ansgar Zoch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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