101
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Schlegel MK, Janas MM, Jiang Y, Barry JD, Davis W, Agarwal S, Berman D, Brown CR, Castoreno A, LeBlanc S, Liebow A, Mayo T, Milstein S, Nguyen T, Shulga-Morskaya S, Hyde S, Schofield S, Szeto J, Woods L, Yilmaz V, Manoharan M, Egli M, Charissé K, Sepp-Lorenzino L, Haslett P, Fitzgerald K, Jadhav V, Maier M. From bench to bedside: Improving the clinical safety of GalNAc-siRNA conjugates using seed-pairing destabilization. Nucleic Acids Res 2022; 50:6656-6670. [PMID: 35736224 PMCID: PMC9262600 DOI: 10.1093/nar/gkac539] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
Preclinical mechanistic studies have pointed towards RNA interference-mediated off-target effects as a major driver of hepatotoxicity for GalNAc-siRNA conjugates. Here, we demonstrate that a single glycol nucleic acid or 2'-5'-RNA modification can substantially reduce small interfering RNA (siRNA) seed-mediated binding to off-target transcripts while maintaining on-target activity. In siRNAs with established hepatotoxicity driven by off-target effects, these novel designs with seed-pairing destabilization, termed enhanced stabilization chemistry plus (ESC+), demonstrated a substantially improved therapeutic window in rats. In contrast, siRNAs thermally destabilized to a similar extent by the incorporation of multiple DNA nucleotides in the seed region showed little to no improvement in rat safety suggesting that factors in addition to global thermodynamics play a role in off-target mitigation. We utilized the ESC+ strategy to improve the safety of ALN-HBV, which exhibited dose-dependent, transient and asymptomatic alanine aminotransferase elevations in healthy volunteers. The redesigned ALN-HBV02 (VIR-2218) showed improved specificity with comparable on-target activity and the program was reintroduced into clinical development.
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Affiliation(s)
| | | | | | | | - Wendell Davis
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Saket Agarwal
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tara Mayo
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Tuyen Nguyen
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Sarah Hyde
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Martin A Maier
- To whom correspondence should be addressed: Tel: +1 617 551 8274; Fax: +1 617 682 4020;
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102
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Bibel B, Elkayam E, Silletti S, Komives EA, Joshua-Tor L. Target binding triggers hierarchical phosphorylation of human Argonaute-2 to promote target release. eLife 2022; 11:76908. [PMID: 35638597 PMCID: PMC9154749 DOI: 10.7554/elife.76908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/26/2022] [Indexed: 12/02/2022] Open
Abstract
Argonaute (Ago) proteins play a central role in post-transcriptional gene regulation through RNA interference (RNAi). Agos bind small RNAs (sRNAs) including small interfering RNAs (siRNAs) and microRNAs (miRNAs) to form the functional core of the RNA-induced silencing complex (RISC). The sRNA is used as a guide to target mRNAs containing either partially or fully complementary sequences, ultimately leading to downregulation of the corresponding proteins. It was previously shown that the kinase CK1α phosphorylates a cluster of residues in the eukaryotic insertion (EI) of Ago, leading to the alleviation of miRNA-mediated repression through an undetermined mechanism. We show that binding of miRNA-loaded human Ago2 to target RNA with complementarity to the seed and 3’ supplementary regions of the miRNA primes the EI for hierarchical phosphorylation by CK1α. The added negative charges electrostatically promote target release, freeing Ago to seek out additional targets once it is dephosphorylated. The high conservation of potential phosphosites in the EI suggests that such a regulatory strategy may be a shared mechanism for regulating miRNA-mediated repression. Proteins are the chemical ‘workhorses’ of the cell: some help maintain a cell’s shape or structure, while others carry out the chemical reactions necessary for life. Organisms therefore need to keep tight control over the production of proteins in their cells, so that the right amount of each protein is made at the right time, in the right place. Instructions for making new proteins are encoded in a type of molecule called messenger RNA. Each messenger RNA contains the instructions for one protein, which are then ‘read’ and carried out by special cellular machinery called ribosomes. The cell can control how much protein it produces by regulating both the levels of different messenger RNA and the amount of protein ribosomes are allowed to make from those instructions. The main way to regulate the levels of messenger RNA is through their transcription from the genome. However, this needs fine tuning. Cells can do this in a highly specific way using molecules called microRNAs. A microRNA works by directing a protein called Argonaute to the messenger RNA that it targets. Once Argonaute arrives, it can call in additional ‘helper proteins’ to shut down, or reduce, protein production from that messenger RNA, or alternatively to break down the messenger RNA altogether. Cells can use an enzyme called CK1α to attach bulky chemical groups onto a specific part of the Argonaute protein, in a reaction termed phosphorylation. The ability to carry out this reaction (and to reverse it) also seems to be important for microRNAs to do their job properly, but why has remained unknown. Bibel et al. wanted to determine what triggers CK1α to phosphorylate Argonaute, and how this affects interactions between microRNAs, Argonaute and their target messenger RNAs. A series of ‘test tube’ experiments looked at the interaction between purified CK1α and Argonaute under different conditions. These demonstrated that CK1α could only carry out its phosphorylation reaction when Argonaute was already interacting with a microRNA and its corresponding messenger RNA. Further measurements revealed that phosphorylation of Argonaute made it detach from the messenger RNA more quickly. This suggests that phosphorylation might be a way to let Argonaute seek out new messenger RNAs after blocking protein production at its first ‘target’. These results shed new light on a fundamental mechanism that cells use to control protein production. Bibel et al. propose that this mechanism may be shared across many different species and could one day help guide the development of new medical therapies based on microRNAs.
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Affiliation(s)
- Brianna Bibel
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Elad Elkayam
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory School of Biological Sciences
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory
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103
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Zhou F, Ebea P, Mutai E, Wang H, Sukreet S, Navazesh S, Dogan H, Li W, Cui J, Ji P, Ramirez DMO, Zempleni J. Small Extracellular Vesicles in Milk Cross the Blood-Brain Barrier in Murine Cerebral Cortex Endothelial Cells and Promote Dendritic Complexity in the Hippocampus and Brain Function in C57BL/6J Mice. Front Nutr 2022; 9:838543. [PMID: 35600828 PMCID: PMC9121399 DOI: 10.3389/fnut.2022.838543] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Human milk contains large amounts of small extracellular vesicles (sEVs) and their microRNA cargos, whereas infant formulas contain only trace amounts of sEVs and microRNAs. We assessed the transport of sEVs across the blood-brain barrier (BBB) and sEV accumulation in distinct regions of the brain in brain endothelial cells and suckling mice. We further assessed sEV-dependent gene expression profiles and effects on the dendritic complexity of hippocampal granule cells and phenotypes of EV depletion in neonate, juvenile and adult mice. The transfer of sEVs across the BBB was assessed by using fluorophore-labeled bovine sEVs in brain endothelial bEnd.3 monolayers and dual chamber systems, and in wild-type newborn pups fostered to sEV and cargo tracking (ECT) dams that express sEVs labeled with a CD63-eGFP fusion protein for subsequent analysis by serial two-photon tomography and staining with anti-eGFP antibodies. Effects of EVs on gene expression and dendritic architecture of granule cells was analyzed in hippocampi from juvenile mice fed sEV and RNA-depleted (ERD) and sEV and RNA-sufficient (ERS) diets by using RNA-sequencing analysis and Golgi-Cox staining followed by integrated neuronal tracing and morphological analysis of neuronal dendrites, respectively. Spatial learning and severity of kainic acid-induced seizures were assessed in mice fed ERD and ERS diets. bEnd.3 cells internalized sEVs by using a saturable transport mechanism and secreted miR-34a across the basal membrane. sEVs penetrated the entire brain in fostering experiments; major regions of accumulation included the hippocampus, cortex and cerebellum. Two hundred ninety-five genes were differentially expressed in hippocampi from mice fed ERD and ERS diets; high-confidence gene networks included pathways implicated in axon guidance and calcium signaling. Juvenile pups fed the ERD diet had reduced dendritic complexity of dentate granule cells in the hippocampus, scored nine-fold lower in the Barnes maze test of spatial learning and memory, and the severity of seizures was 5-fold higher following kainic acid administration in adult mice fed the ERD diet compared to mice fed the ERS diet. We conclude that sEVs cross the BBB and contribute toward optimal neuronal development, spatial learning and memory, and resistance to kainic acid-induced seizures in mice.
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Affiliation(s)
- Fang Zhou
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Pearl Ebea
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Ezra Mutai
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Haichuan Wang
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Sonal Sukreet
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Shya Navazesh
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Haluk Dogan
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Wenhao Li
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Juan Cui
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Peng Ji
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Denise M. O. Ramirez
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
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104
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Duan Y, Veksler-Lublinsky I, Ambros V. Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. Cell Rep 2022; 39:110745. [PMID: 35476978 PMCID: PMC9161110 DOI: 10.1016/j.celrep.2022.110745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 01/21/2022] [Accepted: 04/07/2022] [Indexed: 01/02/2023] Open
Abstract
Base pairing of the seed region (g2–g8) is essential for microRNA targeting; however, the in vivo function of the 3′ non-seed region (g9–g22) is less well understood. Here, we report a systematic investigation of the in vivo roles of 3′ non-seed nucleotides in microRNA let-7a, whose entire g9–g22 region is conserved among bilaterians. We find that the 3′ non-seed sequence functionally distinguishes let-7a from its family paralogs. The complete pairing of g11–g16 is essential for let-7a to fully repress multiple key targets, including evolutionarily conserved lin-41, daf-12, and hbl-1. Nucleotides at g17–g22 are less critical but may compensate for mismatches in the g11–g16 region. Interestingly, a certain minimal complementarity to let-7a 3′ non-seed sequence can be required even for sites with perfect seed pairing. These results provide evidence that the specific configurations of both seed and 3′ non-seed base pairing can critically influence microRNA-mediated gene regulation in vivo. Duan et al. find that microRNA-target pairing at g11–g16 is critical for the function of evolutionarily conserved microRNA let-7a; 3′ pairing is required for both perfect and imperfect seed in regulating multiple targets. These findings provide evidence that base pairing of specific microRNA non-seed nucleotides can critically contribute to target regulation.
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Affiliation(s)
- Ye Duan
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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105
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Li J, Wan H, Zhang H, Wang XL, Liu G, Wu G, He X, Deng Z, Zhao YL. Molecular recognition between bacterial phosphorothioate DNA and sulfur-binding domain (SBD): competition between the water cage and chalcogen-hydrophobic packet. Phys Chem Chem Phys 2022; 24:9176-9187. [PMID: 35383346 DOI: 10.1039/d2cp00291d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial DNA phosphorothioation (PT) physiologically and stereo-specifically replaces a non-bridging oxygen in a phosphate link with a sulfur atom, which can be recognized by a highly conserved sulfur-binding domain (SBD). Here we conducted thermodynamic integration (TI), molecular dynamics simulation, and quantum chemical calculations to decipher the specific molecular interactions between PT-DNA and SBD in Streptomyces coelicolor type IV restriction enzyme ScoMcrA. The TI-calculated binding affinity of (5'-CCGRp-PSGCCGG-3')2 is larger than that of (5'-CCGGCCGG-3')2 by about 7.4-7.7 kcal mol-1. The binding difference dominantly stems from hydration energy of non-phosphorothioate DNA (9.8-10.6 kcal mol-1) in aqueous solution, despite the persistent preference of 2.6-3.2 kcal mol-1 in the DNA-SBD MD simulations. Furthermore, the quantum chemical calculations reveal an unusual non-covalent interaction in the phosphorothioate-binding scenario, where the PS⋯NP165 chalcogen bond prevails the PS⋯HCβ vdW interactions from the adjacent residues H116-R117-Y164-P165-A168. Thus, the chalcogen-hydrophobic interaction pulls PT-DNA into the SBD binding pocket while the water cage pulls a normal DNA molecule out. The synergetic mechanism suggests the special roles of the proline pyrrolidine group in the SBD proteins, consistent with the experimental observations in the X-ray crystallography and structural bioinformatics analysis.
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Affiliation(s)
- Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Haibo Wan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Haoqing Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xiao-Lei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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106
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Neuronal miR-138 Represses HSV-2 Lytic Infection by Regulating Viral and Host Genes with Mechanistic Differences from HSV-1. J Virol 2022; 96:e0034922. [PMID: 35404085 DOI: 10.1128/jvi.00349-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
HSV-1 and HSV-2 are closely related viruses with major differences. Both viruses establish latency in neurons from which they reactivate to cause disease.
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107
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Santovito D, Weber C. Non-canonical features of microRNAs: paradigms emerging from cardiovascular disease. Nat Rev Cardiol 2022; 19:620-638. [PMID: 35304600 DOI: 10.1038/s41569-022-00680-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
Research showing that microRNAs (miRNAs) are versatile regulators of gene expression has instigated tremendous interest in cardiovascular research. The overwhelming majority of studies are predicated on the dogmatic notion that miRNAs regulate the expression of specific target mRNAs by inhibiting mRNA translation or promoting mRNA decay in the RNA-induced silencing complex (RISC). These efforts mostly identified and dissected contributions of multiple regulatory networks of miRNA-target mRNAs to cardiovascular pathogenesis. However, evidence from studies in the past decade indicates that miRNAs also operate beyond this canonical paradigm, featuring non-conventional regulatory functions and cellular localizations that have a pathophysiological role in cardiovascular disease. In this Review, we highlight the functional relevance of atypical miRNA biogenesis and localization as well as RISC heterogeneity. Moreover, we delineate remarkable non-canonical examples of miRNA functionality, including direct interactions with proteins beyond the Argonaute family and their role in transcriptional regulation in the nucleus and in mitochondria. We scrutinize the relevance of non-conventional biogenesis and non-canonical functions of miRNAs in cardiovascular homeostasis and pathology, and contextualize how uncovering these non-conventional properties can expand the scope of translational research in the cardiovascular field and beyond.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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108
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Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids. Int J Mol Sci 2022; 23:ijms23063072. [PMID: 35328493 PMCID: PMC8954656 DOI: 10.3390/ijms23063072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/17/2022] Open
Abstract
The effectiveness of several biological and biotechnological processes relies on the remarkably selective pairing of nucleic acids in contexts of molecular complexity. Relevant examples are the on-target binding of primers in genomic PCR and the regulatory efficacy of microRNA via binding on the transcriptome. Here, we propose a statistical framework that enables us to describe and understand such selectivity by means of a model that is extremely cheap from a computational point of view. By re-parametrizing the hybridization thermodynamics on three classes of base pairing errors, we find a convenient way to obtain the free energy of pairwise interactions between nucleic acids. We thus evaluate the hybridization statistics of a given oligonucleotide within a large number of competitive sites that we assume to be random, and we compute the probability of on-target binding. We apply our strategy to PCR amplification and microRNA-based gene regulation, shedding new light on their selectivity. In particular, we show the relevance of the defectless pairing of 3′ terminals imposed by the polymerase in PCR selection. We also evaluate the selectivity afforded by the microRNA seed region, thus quantifying the extra contributions given by mechanisms beyond pairing statistics.
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109
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Ober-Reynolds B, Becker WR, Jouravleva K, Jolly SM, Zamore PD, Greenleaf WJ. High-throughput biochemical profiling reveals functional adaptation of a bacterial Argonaute. Mol Cell 2022; 82:1329-1342.e8. [PMID: 35298909 PMCID: PMC9158488 DOI: 10.1016/j.molcel.2022.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/10/2022] [Accepted: 02/16/2022] [Indexed: 12/29/2022]
Abstract
Argonautes are nucleic acid-guided proteins that perform numerous cellular functions across all domains of life. Little is known about how distinct evolutionary pressures have shaped each Argonaute's biophysical properties. We applied high-throughput biochemistry to characterize how Thermus thermophilus Argonaute (TtAgo), a DNA-guided DNA endonuclease, finds, binds, and cleaves its targets. We found that TtAgo uses biophysical adaptations similar to those of eukaryotic Argonautes for rapid association but requires more extensive complementarity to achieve high-affinity target binding. Using these data, we constructed models for TtAgo association rates and equilibrium binding affinities that estimate the nucleic acid- and protein-mediated components of the target interaction energies. Finally, we showed that TtAgo cleavage rates vary widely based on the DNA guide, suggesting that only a subset of guides cleaves targets on physiologically relevant timescales.
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Affiliation(s)
| | - Winston R Becker
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Karina Jouravleva
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samson M Jolly
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Chan 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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110
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Zhuang H, Fan X, Ji D, Wang Y, Fan J, Li M, Ni D, Lu S, Li X, Chai Z. Elucidation of the conformational dynamics and assembly of Argonaute-RNA complexes by distinct yet coordinated actions of the supplementary microRNA. Comput Struct Biotechnol J 2022; 20:1352-1365. [PMID: 35356544 PMCID: PMC8933676 DOI: 10.1016/j.csbj.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Argonaute (AGO) proteins, the core of RNA-induced silencing complex, are guided by microRNAs (miRNAs) to recognize target RNA for repression. The miRNA-target RNA recognition forms initially through pairing at the seed region while the additional supplementary pairing can enhance target recognition and compensate for seed mismatch. The extension of miRNA lengths can strengthen the target affinity when pairing both in the seed and supplementary regions. However, the mechanism underlying the effect of the supplementary pairing on the conformational dynamics and the assembly of AGO-RNA complex remains poorly understood. To address this, we performed large-scale molecular dynamics simulations of AGO-RNA complexes with different pairing patterns and miRNA lengths. The results reveal that the additional supplementary pairing can not only strengthen the interaction between miRNA and target RNA, but also induce the increased plasticity of the PAZ domain and enhance the domain connectivity among the PAZ, PIWI, N domains of the AGO protein. The strong community network between these domains tightens the mouth of the supplementary chamber of AGO protein, which prevents the escape of target RNA from the complex and shields it from solvent water attack. Importantly, the inner stronger matching pairs between the miRNA and target RNA can compensate for weaker mismatches at the edge of supplementary region. These findings provide guidance for the design of miRNA mimics and anti-miRNAs for both clinical and experimental use and open the way for further engineering of AGO proteins as a new tool in the field of gene regulation.
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Affiliation(s)
- Haiming Zhuang
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xiaohua Fan
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yuanhao Wang
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200438, China
- Department of Hepatic Surgery, Shanghai Geriatric Center, Shanghai 201104, China
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111
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Yang T, Wang J, Zhao J, Liu Y. Current and prospective applications of exosomal microRNAs in pulmonary fibrosis (Review). Int J Mol Med 2022; 49:37. [PMID: 35088880 PMCID: PMC8815412 DOI: 10.3892/ijmm.2022.5092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022] Open
Abstract
Pulmonary fibrosis (PF) is a chronic, progressive, irreversible and life‑threatening lung disease. However, the pathogenesis and molecular mechanisms of this condition remain unclear. Extracellular vesicles (EVs) are structures derived from the plasma membrane, with a diameter ranging from 30 nm to 5 µm, that play an important role in cell‑to‑cell communications in lung disease, particularly between epithelial cells and the pulmonary microenvironment. In particular, exosomes are a type of EV that can deliver cargo molecules, including endogenous proteins, lipids and nucleic acids, such as microRNAs (miRNAs/miRs). These cargo molecules are encapsulated in lipid bilayers through target cell internalization, receptor‑ligand interactions or lipid membrane fusion. miRNAs are single‑stranded RNA molecules that regulate cell differentiation, proliferation and apoptosis by degrading target mRNAs or inhibiting translation to modulate gene expression. The aim of the present review was to discuss the current knowledge available on exosome biogenesis, composition and isolation methods. The role of miRNAs in the pathogenesis of PF was also reviewed. In addition, emerging diagnostic and therapeutic properties of exosomes and exosomal miRNAs in PF were described, in order to highlight the potential applications of exosomal miRNAs in PF.
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Affiliation(s)
- Tao Yang
- Department of Respiratory and Critical Care Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
- The First Clinical Medical School of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Jian Wang
- Department of Respiratory and Critical Care Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Jiaying Zhao
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Yang Liu
- Department of Respiratory and Critical Care Medicine, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
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112
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Zogg H, Singh R, Ro S. Current Advances in RNA Therapeutics for Human Diseases. Int J Mol Sci 2022; 23:2736. [PMID: 35269876 PMCID: PMC8911101 DOI: 10.3390/ijms23052736] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Following the discovery of nucleic acids by Friedrich Miescher in 1868, DNA and RNA were recognized as the genetic code containing the necessary information for proper cell functioning. In the years following these discoveries, vast knowledge of the seemingly endless roles of RNA have become better understood. Additionally, many new types of RNAs were discovered that seemed to have no coding properties (non-coding RNAs), such as microRNAs (miRNAs). The discovery of these new RNAs created a new avenue for treating various human diseases. However, RNA is relatively unstable and is degraded fairly rapidly once administered; this has led to the development of novel delivery mechanisms, such as nanoparticles to increase stability as well as to prevent off-target effects of these molecules. Current advances in RNA-based therapies have substantial promise in treating and preventing many human diseases and disorders through fixing the pathology instead of merely treating the symptomology similarly to traditional therapeutics. Although many RNA therapeutics have made it to clinical trials, only a few have been FDA approved thus far. Additionally, the results of clinical trials for RNA therapeutics have been ambivalent to date, with some studies demonstrating potent efficacy, whereas others have limited effectiveness and/or toxicity. Momentum is building in the clinic for RNA therapeutics; future clinical care of human diseases will likely comprise promising RNA therapeutics. This review focuses on the current advances of RNA therapeutics and addresses current challenges with their development.
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Affiliation(s)
| | | | - Seungil Ro
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, 1664 North Virginia Street, Reno, NV 89557, USA; (H.Z.); (R.S.)
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113
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McGeary SE, Bisaria N, Pham TM, Wang PY, Bartel DP. MicroRNA 3'-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position. eLife 2022; 11:e69803. [PMID: 35191832 PMCID: PMC8940178 DOI: 10.7554/elife.69803] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2-8), preferences of the miRNA 3' region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2-miRNA complexes to measure relative affinities of >1000 3'-pairing architectures for each miRNA. In some cases, optimal 3' pairing increased affinity by >500 fold. Some miRNAs had two high-affinity 3'-pairing modes-one of which included additional nucleotides bridging seed and 3' pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3' pairing is determined for each miRNA.
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Affiliation(s)
- Sean E McGeary
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Namita Bisaria
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Thy M Pham
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Peter Y Wang
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - David P Bartel
- Howard Hughes Medical InstituteCambridgeUnited States
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
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114
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Soutschek M, Gross F, Schratt G, Germain PL. scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction. Bioinformatics 2022; 38:2466-2473. [PMID: 35188178 DOI: 10.1093/bioinformatics/btac110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/22/2022] [Accepted: 02/17/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived k-mer affinity predictions, however these findings are not easily applicable. RESULTS We translate this approach into a flexible and user-friendly bioconductor package, scanMiR, also available through a web interface. Using lightweight linear models, scanMiR efficiently scans for binding sites, estimates their affinity, and predicts aggregated transcript repression. Moreover, flexible 3'-supplementary alignment enables the prediction of unconventional interactions, such as bindings potentially leading to target-directed microRNA degradation or slicing. We showcase scanMiR through a systematic scan for such unconventional sites on neuronal transcripts, including lncRNAs and circRNAs. Finally, in addition to the main bioconductor package implementing these functions, we provide a user-friendly web application enabling the scanning of sequences, the visualization of predicted bindings, and the browsing of predicted target repression. AVAILABILITY scanMiR and companion packages are implemented in R, released under the GPL-3 and accessible on Bioconductor (https://bioconductor.org/packages/release/bioc/html/scanMiR.html) as well as through a shiny web server (https://ethz-ins.org/scanMiR/). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Fridolin Gross
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Lab of Statistical Bioinformatics, IMLS, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
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115
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Zhang Z, Wu Y, Lin N, Yin S, Meng Z. Monitoring Clinical-Pathological Grading of Hepatocellular Carcinoma Using MicroRNA-Guided Semiconducting Polymer Dots. ACS APPLIED MATERIALS & INTERFACES 2022; 14:7717-7730. [PMID: 35112844 DOI: 10.1021/acsami.1c24191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNAs involved in nearly all genetic central dogma processes and human biological behavior, which also play a significant role in the pathological activity of tumors, such as gene transcription, protein translation, and exosome secretion. Therefore, through the navigation of certain specific miRNAs, we can trace the specific physiological processes or image some specific tissues. Designing and accurately positioning microRNA (miRNA)-sensitive fluorescent nanoprobes with benign specificity and recognition in cells or tissues are a challenging research field. To solve the difficulties, we introduce four semiconducting polymer dots (Pdots) as nanoprobes linked by specific miRNA antisense sequences for monitoring the pathological grading by the variation in miRNA expression. Based on the base pairing principle, these miRNA-sensitive Pdots could bind to specific miRNAs within the cancerous cells. As impacted by the background of different pathology gradings, the proportions of the four hepatocellular carcinoma (HCC)-specific miRNAs within the cancerous cell are different, and the pathological grading of the patient tissues can be determined by comparing the palette combinations. The short single-stranded RNA-functionalized Pdots, which have excellent microRNA sensitivity, are observed in an experimental cell model and a series of tissue specimens from HCC patients for the first time. Using the Förster (or fluorescence) resonance energy transfer (FRET) model of Pdots and Cy3dt tag to simulate in vivo miRNA detection, the superior sensitivity and specificity of these nanoprobes are verified. The interference of subjective factors in traditional single/bis-dye emission intensity detection is abandoned, and multiple label staining is used to enhance sensitivity further and reduce the false-positive rate. The feasibility exhibited by this novel staining method is verified in normal hepatocellular HCC cell lines and 16 frozen ultrathin tissue sections, which are employed to quantify pathological grading-related color presentation systems for clinical doctors and pathologists' use. The intelligently designed miRNA-guided Pdots will emerge as an ideal platform with promising biological imaging.
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Affiliation(s)
- Ze Zhang
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Jilin University, No. 126 Xiantai Street, Changchun, Jilin 130000, P. R. China
| | - Yuyang Wu
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Nan Lin
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Shengyan Yin
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Zihui Meng
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Jilin University, No. 126 Xiantai Street, Changchun, Jilin 130000, P. R. China
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116
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Zhang Y, Zhang Y, Ai B, Gong J, Li Y, Yu S, Cai X, Zhang L. GTF2E2 is a novel biomarker for recurrence after surgery and promotes progression of esophageal squamous cell carcinoma via miR-139-5p/GTF2E2/FUS axis. Oncogene 2022; 41:782-796. [PMID: 34853466 PMCID: PMC8816730 DOI: 10.1038/s41388-021-02122-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal gastrointestinal malignancies with high mortality. Recurrence develops within only a few years after curative resection and perioperative adjuvant therapy in 30-50% of these patients. Therefore, it is essential to identify postoperative recurrence biomarkers to facilitate selecting the following surveillance and therapeutic strategies. The general transcription factor IIE subunit beta (GTF2E2) is crucial for physiological and pathological functions, but its roles in the aggression and recurrence of ESCC remain ambiguous. In this study, we found that GTF2E2 was highly expressed in ESCC samples, and elevated GTF2E2 expression predicted early recurrence after surgery for ESCC patients. High expression of GTF2E2 associated with more aggressive clinic features and poor prognosis. GTF2E2 promoted the proliferation and mobility of ESCC cells in vitro and in vivo. We further revealed that miR-139-5p repressed GTF2E2 expression by downregulating its mRNA through binding with Argonaute 2 (Ago2). Rescue assays suggested that miR-139-5p affected GTF2E2-mediated ESCC progression. Moreover, GTF2E2 positively interacted with FUS promoter and regulated FUS expression, and the phenotype changes caused by GTF2E2 manipulation were recovered by rescuing FUS expression in ESCC cells. Additionally, we demonstrated that GTF2E2 promotes ESCC cells progression via activation of the AKT/ERK/mTOR pathway. In conclusion, GTF2E2 may serve as a novel biomarker for recurrence after surgery and a potential therapeutic target for ESCC patients, and it promotes ESCC progression via miR-139-5p/GTF2E2/FUS axis.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Middle Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/genetics
- Disease Progression
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/pathology
- Esophageal Neoplasms/surgery
- Esophageal Neoplasms/metabolism
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Squamous Cell Carcinoma/surgery
- Esophageal Squamous Cell Carcinoma/metabolism
- Gene Expression Regulation, Neoplastic
- Mice, Nude
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/metabolism
- Prognosis
- Transcription Factors, TFII/genetics
- Transcription Factors, TFII/metabolism
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Affiliation(s)
- Yujie Zhang
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yuxin Zhang
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Bo Ai
- Thoracic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Juejun Gong
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Yichen Li
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Shiying Yu
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
| | - Xiuyu Cai
- Department of VIP Inpatient, Sun Yet-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, No.651 Dongfeng Road East, Guangzhou, Guangdong, 510060, P. R. China.
| | - Li Zhang
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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117
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Zhang J, Chen S, Liu K. Structural insights into piRNA biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194799. [PMID: 35182819 DOI: 10.1016/j.bbagrm.2022.194799] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/24/2023]
Abstract
Discovered two decades ago, Piwi-interacting RNAs (piRNAs) play critical roles in gene regulation, transposon element repression, and antiviral defense. Dysregulation of piRNAs has been noted in diverse human diseases including cancers. Recently, extensive studies have revealed that many more proteins are involved in piRNA biogenesis. This review will summarize the recent progress in piRNA biogenesis and functions, especially the molecular mechanisms by which piRNA biogenesis-related proteins contribute to piRNA processing.
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Affiliation(s)
- Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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118
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Takegawa-Araki T, Kumagai S, Yasukawa K, Kuroda M, Sasaki T, Obika S. Structure-Activity Relationships of Anti-microRNA Oligonucleotides Containing Cationic Guanidine-Modified Nucleic Acids. J Med Chem 2022; 65:2139-2148. [PMID: 35084859 DOI: 10.1021/acs.jmedchem.1c01680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anti-microRNA oligonucleotides (AMOs) are valuable tools for the treatment of diseases caused by the dysregulation of microRNA expression. However, the correlation between chemical modifications in AMO sequences and the microRNA-inhibitory activity has not been fully elucidated. In this study, we synthesized a series of AMOs containing cationic guanidine-bridged nucleic acids (GuNA) and evaluated their activities using a dual luciferase assay. We also optimized the site of GuNA substitution and found an effective design for the inhibition of microRNA-21, which was partially different from that of conventional nucleic acid derivatives. This study showed that GuNA-substituted AMOs are effective in inhibiting the function of microRNA.
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Affiliation(s)
- Tomo Takegawa-Araki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Shinji Kumagai
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Kai Yasukawa
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Masataka Kuroda
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Takashi Sasaki
- Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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119
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Mutai E, Ngu AKH, Zempleni J. Preliminary evidence that lectins in infant soy formula apparently bind bovine milk exosomes and prevent their absorption in healthy adults. BMC Nutr 2022; 8:7. [PMID: 35063038 PMCID: PMC8780320 DOI: 10.1186/s40795-022-00503-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/14/2022] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
Milk exosomes and their microRNA (miR) cargos are bioavailable. The content of exosomes and miRs is negligible in infant formulas compared to human milk, and dietary depletion of exosomes led to changes in bacterial communities and impaired gut health in juvenile mice. Adverse effects of formula feeding may be compounded by using soy formulas due to exosome binding by abundant lectins in that matrix. The purpose of this study was to assess the bioavailability of milk exosomes and their miR cargos added to soy formula in adults, as well as the potential role of soy lectins in exosome bioavailability.
Methods
Eleven healthy adults (6 men, 5 women) enrolled in this randomized crossover study. Participants consumed 1.0 l of soy formula without (SF) or with (SFE) bovine milk exosomes added. Concentration-time curves of six plasma miRs were analyzed using reverse transcription quantitative PCR. Lectin affinity chromatography was used to assess the binding of exosomes by soy lectins. Data were analyzed by using paired t test. P < 0.05 was considered statistically significant.
Results
Consumption of SF and SFE did not elicit postprandial increases in plasma miRs. Approximately 39% of bovine milk exosome particles were retained by lectin columns.
Conclusions
We conclude that fortification of soy formulas with milk exosomes, in the absence of removing lectins, is not a viable strategy for delivering bioavailable exosomes and their miR cargos. Lectins in soy formulas bind glycoprotein on the surfaces of milk exosomes, thereby preventing exosome absorption.
Trial registration
ISRCTN registry ID: 16329971. Retrospectively registered on February 7th, 2019.
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120
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Kobayashi Y, Fukuhara D, Akase D, Aida M, Ui-Tei K. siRNA Seed Region Is Divided into Two Functionally Different Domains in RNA Interference in Response to 2'-OMe Modifications. ACS OMEGA 2022; 7:2398-2410. [PMID: 35071927 PMCID: PMC8771963 DOI: 10.1021/acsomega.1c06455] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/24/2021] [Indexed: 05/04/2023]
Abstract
In RNA interference (RNAi), small interfering RNA (siRNA) functions to suppress the expression of its target mRNA with perfect sequence complementarity. In a mechanism different from above, siRNA also suppresses unintended mRNAs with partial sequence complementarities, mainly to the siRNA seed region (nucleotides 2-8). This mechanism is largely utilized by microRNAs (miRNAs) and results in siRNA-mediated off-target effects. Thus, the siRNA seed region is considered to be involved in both RNAi and off-target effects. In this study, we revealed that the impact of 2'-O-methyl (2'-OMe) modification is different according to the nucleotide positions. The 2'-OMe modifications of nucleotides 2-5 inhibited off-target effects without affecting on-target RNAi activities. In contrast, 2'-OMe modifications of nucleotides 6-8 increased both RNAi and off-target activities. The computational simulation revealed that the structural change induced by 2'-OMe modifications interrupts base pairing between siRNA and target/off-target mRNAs at nucleotides 2-5 but enhances at nucleotides 6-8. Thus, our results suggest that siRNA seed region consists of two functionally different domains in response to 2'-OMe modifications: nucleotides 2-5 are essential for avoiding off-target effects, and nucleotides 6-8 are involved in the enhancement of both RNAi and off-target activities.
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Affiliation(s)
- Yoshiaki Kobayashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Daiki Fukuhara
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dai Akase
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Misako Aida
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kumiko Ui-Tei
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department
of Computational Biology and Medical Sciences, Graduate School of
Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
- . Phone: +81-3-5841-3044. Fax: +81-3-5841-3044
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121
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Leitão AL, Enguita FJ. A Structural View of miRNA Biogenesis and Function. Noncoding RNA 2022; 8:ncrna8010010. [PMID: 35202084 PMCID: PMC8874510 DOI: 10.3390/ncrna8010010] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022] Open
Abstract
Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.
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Affiliation(s)
- Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
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122
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Peterson KJ, Beavan A, Chabot PJ, McPeek MA, Pisani D, Fromm B, Simakov O. MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events. Mol Biol Evol 2022; 39:msab344. [PMID: 34865078 PMCID: PMC8789304 DOI: 10.1093/molbev/msab344] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Whole-genome duplications (WGDs) have long been considered the causal mechanism underlying dramatic increases to morphological complexity due to the neo-functionalization of paralogs generated during these events. Nonetheless, an alternative hypothesis suggests that behind the retention of most paralogs is not neo-functionalization, but instead the degree of the inter-connectivity of the intended gene product, as well as the mode of the WGD itself. Here, we explore both the causes and consequences of WGD by examining the distribution, expression, and molecular evolution of microRNAs (miRNAs) in both gnathostome vertebrates as well as chelicerate arthropods. We find that although the number of miRNA paralogs tracks the number of WGDs experienced within the lineage, few of these paralogs experienced changes to the seed sequence, and thus are functionally equivalent relative to their mRNA targets. Nonetheless, in gnathostomes, although the retention of paralogs following the 1R autotetraploidization event is similar across the two subgenomes, the paralogs generated by the gnathostome 2R allotetraploidization event are retained in higher numbers on one subgenome relative to the second, with the miRNAs found on the preferred subgenome showing both higher expression of mature miRNA transcripts and slower molecular evolution of the precursor miRNA sequences. Importantly, WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
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Affiliation(s)
- Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Alan Beavan
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Bastian Fromm
- Arctic University Museum of Norway, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
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123
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Singh G, Mallick B. Predicting sequence and structural features of effective piRNA target binding sites. J Mol Recognit 2022; 35:e2949. [PMID: 34979054 DOI: 10.1002/jmr.2949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022]
Abstract
Piwi-interacting RNA (piRNA) targets are usually identified through base pairing between the piRNA seed region and complementary bases on the target mRNAs, which often results in false predictions. Crosslinking immunoprecipitation (CLIP) study emerges as a promising method that enables accurate identification of PIWI-clade-based targets containing RNA-binding sites. In the present study, we have analyzed the piRNA-target CLIP-seq datasets to uncover the additional characteristic features of piRNA targets. We studied important sequence and structural features using IP+ and IP- set targets that might enhance the accuracy of target site predictions. Analysis has revealed substantial enrichment of AU in target sites as well as in and around the 30 nts upstream and downstream of target sites in IP+ set relative to IP- set that might be contributing to lowering the minimal folding energy of target sites of IP+ + set that might be easing the base pairing between piRNA and their targets. We have also found a lower MFE threshold (en) and higher miRanda score for piRNA targets. Interestingly, we have found that majority of the target sites are residing within 3'UTR, suggesting 3'UTR as a preferential target site like that of miRNA targets. Thus, we hypothesize that our findings on additional key features of piRNA target sites might be valuable in identifying the potential targets of piRNA accurately, which will aid in decrypting their functional importance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Garima Singh
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, India
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124
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Lin Q, Shi Y, Liu Z, Mehrpour M, Hamaï A, Gong C. Non-coding RNAs as new autophagy regulators in cancer progression. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166293. [PMID: 34688868 DOI: 10.1016/j.bbadis.2021.166293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/17/2021] [Accepted: 10/10/2021] [Indexed: 12/09/2022]
Abstract
Recent advances highlight that non-coding RNAs (ncRNAs) are emerging as fundamental regulators in various physiological as well as pathological processes by regulating macro-autophagy. Studies have disclosed that macro-autophagy, which is a highly conserved process involving cellular nutrients, components, and recycling of organelles, can be either selective or non-selective and ncRNAs show their regulation on selective autophagy as well as non-selective autophagy. The abnormal expression of ncRNAs will result in the impairment of autophagy and contribute to carcinogenesis and cancer progression by regulating both selective autophagy as well as non-selective autophagy. This review focuses on the regulatory roles of ncRNAs in autophagy and their involvement in cancer which may provide valuable therapeutic targets for cancer management.
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Affiliation(s)
- Qun Lin
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Yu Shi
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Zihao Liu
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China
| | - Maryam Mehrpour
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, 75993, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75993 Paris, France
| | - Ahmed Hamaï
- Institut Necker-Enfants Malades (INEM), Inserm U1151-CNRS UMR 8253, 75993, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75993 Paris, France
| | - Chang Gong
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Bioland Laboratory, 510005 Guangzhou, China.
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125
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3D Modeling of Non-coding RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:281-317. [DOI: 10.1007/978-3-031-08356-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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126
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Kropocheva EV, Lisitskaya LA, Agapov AA, Musabirov AA, Kulbachinskiy AV, Esyunina DM. Prokaryotic Argonaute Proteins as a Tool for Biotechnology. Mol Biol 2022; 56:854-873. [PMID: 36060308 PMCID: PMC9427165 DOI: 10.1134/s0026893322060103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Programmable nucleases are the most important tool for manipulating the genes and genomes of both prokaryotes and eukaryotes. Since the end of the 20th century, many approaches were developed for specific modification of the genome. The review briefly considers the advantages and disadvantages of the main genetic editors known to date. The main attention is paid to programmable nucleases from the family of prokaryotic Argonaute proteins. Argonaute proteins can recognize and cleave DNA sequences using small complementary guide molecules and play an important role in protecting prokaryotic cells from invading DNA. Argonaute proteins have already found applications in biotechnology for targeted cleavage and detection of nucleic acids and can potentially be used for genome editing.
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Affiliation(s)
- E. V. Kropocheva
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - L. A. Lisitskaya
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. A. Agapov
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. A. Musabirov
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. V. Kulbachinskiy
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - D. M. Esyunina
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
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127
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Skeparnias I, Zhang J. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Noncoding RNA 2021; 7:ncrna7040081. [PMID: 34940761 PMCID: PMC8704770 DOI: 10.3390/ncrna7040081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation. By contrast, the nature of these interactions and characteristics of their interfaces, especially those that involve partially or wholly structured RNAs, remain elusive. Herein, we discuss different modalities of RNA–RNA interactions with an emphasis on those that depend on secondary, tertiary, or quaternary structure. We dissect recently structurally elucidated RNA–RNA complexes including RNA triplexes, riboswitches, ribozymes, and reverse transcription complexes. These analyses highlight a reciprocal relationship that intimately links RNA structure formation with RNA–RNA interactions. The interactions not only shape and sculpt RNA structures but also are enabled and modulated by the structures they create. Understanding this two-way relationship between RNA structure and interactions provides mechanistic insights into the expanding repertoire of noncoding RNA functions, and may inform the design of novel therapeutics that target RNA structures or interactions.
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128
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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: 217] [Impact Index Per Article: 54.3] [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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129
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Yamada K, Hildebrand S, Davis SM, Miller R, Conroy F, Sapp E, Caiazzi J, Alterman JF, Roux L, Echeverria D, Hassler MR, Pfister EL, DiFiglia M, Aronin N, Khvorova A. Structurally constrained phosphonate internucleotide linkage impacts oligonucleotide-enzyme interaction, and modulates siRNA activity and allele specificity. Nucleic Acids Res 2021; 49:12069-12088. [PMID: 34850120 PMCID: PMC8643693 DOI: 10.1093/nar/gkab1126] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/09/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Oligonucleotides is an emerging class of chemically-distinct therapeutic modalities, where extensive chemical modifications are fundamental for their clinical applications. Inter-nucleotide backbones are critical to the behaviour of therapeutic oligonucleotides, but clinically explored backbone analogues are, effectively, limited to phosphorothioates. Here, we describe the synthesis and bio-functional characterization of an internucleotide (E)-vinylphosphonate (iE-VP) backbone, where bridging oxygen is substituted with carbon in a locked stereo-conformation. After optimizing synthetic pathways for iE-VP-linked dimer phosphoramidites in different sugar contexts, we systematically evaluated the impact of the iE-VP backbone on oligonucleotide interactions with a variety of cellular proteins. Furthermore, we systematically evaluated the impact of iE-VP on RNA-Induced Silencing Complex (RISC) activity, where backbone stereo-constraining has profound position-specific effects. Using Huntingtin (HTT) gene causative of Huntington's disease as an example, iE-VP at position 6 significantly enhanced the single mismatch discrimination ability of the RISC without negative impact on silencing of targeting wild type htt gene. These findings suggest that the iE-VP backbone can be used to modulate the activity and specificity of RISC. Our study provides (i) a new chemical tool to alter oligonucleotide-enzyme interactions and metabolic stability, (ii) insight into RISC dynamics and (iii) a new strategy for highly selective SNP-discriminating siRNAs.
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Affiliation(s)
- Ken Yamada
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Samuel Hildebrand
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Faith Conroy
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Edith L Pfister
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marian DiFiglia
- Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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130
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Zhu L, Jiang H, Cao S, Unarta IC, Gao X, Huang X. Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Commun Biol 2021; 4:1345. [PMID: 34848812 PMCID: PMC8632932 DOI: 10.1038/s42003-021-02822-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
Despite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.
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Affiliation(s)
- Lizhe Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, 518172, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Siqin Cao
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Ilona Christy Unarta
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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131
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Pourjafar-Dehkordi D, Zacharias M. Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling. PLoS Comput Biol 2021; 17:e1009625. [PMID: 34843451 PMCID: PMC8683029 DOI: 10.1371/journal.pcbi.1009625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/17/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022] Open
Abstract
Argonaute proteins in combination with short microRNA (miRNAs) can target mRNA molecules for translation inhibition or degradation and play a key role in many regulatory processes. The miRNAs act as guide RNAs that associate with Argonaute and the complementary mRNA target region. The complex formation results in activation of Argonaute and specific cleavage of the target mRNA. Both the binding and activation processes involve essential domain rearrangements of functional importance. For the Thermus Thermophilus Argonaute (TtAgo) system guide-bound (binary) and guide/target-bound (ternary) complexes are known but how the binding of guide and target mediate domain movements is still not understood. We have studied the Argonaute domain motion in apo and guide/target bound states using Molecular Dynamics simulations and a Hamiltonian replica exchange (H-REMD) method that employs a specific biasing potential to accelerate domain motions. The H-REMD technique indicates sampling of a much broader distribution of domain arrangements both in the apo as well as binary and ternary complexes compared to regular MD simulations. In the apo state domain arrangements corresponding to more compact (closed) states are mainly sampled which undergo an opening upon guide and guide/target binding. Whereas only limited overlap in domain geometry between apo and bound states was found, a larger similarity in the domain distribution is observed for the simulations of binary and ternary complexes. Comparative simulations on ternary complexes with 15 or 16 base pairs (bp) formed between guide and target strands (instead of 14) resulted in dissociation of the 3’-guide strand from the PAZ domain and domain rearrangement. This agrees with the experimental observation that guide-target pairing beyond 14 bps is required for activation and gives a mechanistic explanation for the experimentally observed activation process. Post-transcriptional gene silencing is an important process to regulate protein synthesis in eukaryotes and prokaryotes. The Argonaute proteins as part of the RNA-induced-silencing-complex (RISC) form a central element of the process by silencing of a target messenger RNA (mRNA) via degradation or repression of translation. The Argonaute protein binds initially a short RNA that acts as a guide to promote binding of a complementary target mRNA. The complex formation can lead to activation of Argonaute and specific cleavage of the target mRNA. The whole process involves domain rearrangements that are not fully understood. We applied an advanced Molecular Dynamics sampling technique to specifically accelerate domain motions of the Thermus Thermophilus Argonaute (TtAgo) system in apo, guide bound and guide/target bound states. The simulations indicate only limited overlap of domain arrangements in apo and bound states and identified domain opening motions necessary for guide and target binding. The study also offers an explanation why a minimum of 15 or 16 base pairs between guide and target strands are necessary for Argonaute activation.
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Affiliation(s)
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technische Universität München, Garching, Germany
- * E-mail:
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132
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A structured RNA motif locks Argonaute2:miR-122 onto the 5' end of the HCV genome. Nat Commun 2021; 12:6836. [PMID: 34824224 PMCID: PMC8616905 DOI: 10.1038/s41467-021-27177-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/27/2021] [Indexed: 12/03/2022] Open
Abstract
microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex. The RNA genome of the Hepatitis C Virus binds to the liver-specific miR122. Here the authors report the crystal structure of the Ago2:miR122:HCV complex showing that the viral RNA’s structural element traps the Ago2:miR-122 complex on the 5’ end of the viral genome to protect it from degradation.
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133
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Schlegel MK, Matsuda S, Brown CR, Harp JM, Barry JD, Berman D, Castoreno A, Schofield S, Szeto J, Manoharan M, Charissé K, Egli M, Maier MA. Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs. Nucleic Acids Res 2021; 49:10851-10867. [PMID: 34648028 PMCID: PMC8565336 DOI: 10.1093/nar/gkab916] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
We recently reported that RNAi-mediated off-target effects are important drivers of the hepatotoxicity observed for a subset of GalNAc–siRNA conjugates in rodents, and that these findings could be mitigated by seed-pairing destabilization using a single GNA nucleotide placed within the seed region of the guide strand. Here, we report further investigation of the unique and poorly understood GNA/RNA cross-pairing behavior to better inform GNA-containing siRNA design. A reexamination of published GNA homoduplex crystal structures, along with a novel structure containing a single (S)-GNA-A residue in duplex RNA, indicated that GNA nucleotides universally adopt a rotated nucleobase orientation within all duplex contexts. Such an orientation strongly affects GNA-C and GNA-G but not GNA-A or GNA-T pairing in GNA/RNA heteroduplexes. Transposition of the hydrogen-bond donor/acceptor pairs using the novel (S)-GNA-isocytidine and -isoguanosine nucleotides could rescue productive base-pairing with the complementary G or C ribonucleotides, respectively. GalNAc-siRNAs containing these GNA isonucleotides showed an improved in vitro activity, a similar improvement in off-target profile, and maintained in vivo activity and guide strand liver levels more consistent with the parent siRNAs than those modified with isomeric GNA-C or -G, thereby expanding our toolbox for the design of siRNAs with minimized off-target activity.
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Affiliation(s)
| | | | | | - Joel M Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Daniel Berman
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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134
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Li W, Soufiany I, Lyu X, Lu C, Wei Y, Shi Z, You Y. SP1-upregulated LBX2-AS1 promotes the progression of glioma by targeting the miR-491-5p/LIF axis. J Cancer 2021; 12:6989-7002. [PMID: 34729101 PMCID: PMC8558668 DOI: 10.7150/jca.63289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Mounting evidences have shown the importance of lncRNAs in carcinogenesis and cancer progression. LBX2-AS1 is identified as an oncogenic lncRNA that is abnormally expressed in gastric cancer and lung cancer samples. This study aims to explore the potential role of LBX2-AS1 in regulating proliferation and EMT in glioma, and the underlying mechanism. Methods: Relative levels of LBX2-AS1 in glioma samples and cell lines were detected by qRT-PCR and FISH. In vivo and in vitro regulatory effects of LBX2-AS1 on proliferation and EMT were examined in the xenograft glioma model and glioma cells. The interaction between SP1 and LBX2-AS1 was assessed by ChIP. Through bioinformatic analyses, dual-luciferase reporter assay, RIP and Western blot, the regulation of LBX2-AS1 and miR-491-5p on the target gene LIF was identified. Results: LBX2-AS1 was upregulated in glioma samples and cell lines, and its transcription was promoted by binding to the transcription factor SP1. As a lncRNA mainly distributed in the cytoplasm, LBX2-AS1 sponge miR-491-5p to further upregulate LIF. The subsequent activated LIF/STAT3 signaling was responsible for promoting proliferation and EMT in glioma. Conclusion: LBX2-AS1 is upregulated by SP1 in glioma, which promotes the progression of glioma by targeting the miR-491-5p/LIF axis. In view of this, LBX2-AS1 is suggested as a novel diagnostic biomarker and therapeutic target of glioma.
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Affiliation(s)
- Wentao Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Ismatullah Soufiany
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Xiao Lyu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Chenfei Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Yutian Wei
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Zhumei Shi
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.,Institute for Brain Tumors, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China.,Institute for Brain Tumors, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
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135
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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136
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Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, Plavec J, Egli M, Manoharan M, Zlatev I. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Res 2021; 49:10250-10264. [PMID: 34508350 PMCID: PMC8501968 DOI: 10.1093/nar/gkab724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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137
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Learning noncoding RNA biology from viruses. Mamm Genome 2021; 33:412-420. [PMID: 34491378 DOI: 10.1007/s00335-021-09915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Insights into interactions between viral factors and the cellular machinery usually lead to discoveries concerning host cell biology. Thus, the gene expression field has historically relied on viral model systems to discover mechanisms underlying different cellular processes. In recent years, the functional characterization of the small nuclear noncoding RNAs expressed by the oncogenic Herpesvirus saimiri, called HSURs, resulted in the discovery of two mechanisms for the regulation of gene expression. HSUR1 and HSUR2 associate with host microRNAs, which are small noncoding RNAs that broadly regulate gene expression by binding to messenger RNAs. HSUR1 provided the first example of a process known as target-directed miRNA degradation that operates in cells to regulate miRNA populations. HSUR2 functions as a miRNA adaptor, uncovering an entirely new, indirect mechanism by which miRNAs can inhibit mRNA function. Here, I review the path that led to these discoveries and their implications and postulate new exciting questions about the functions of these fascinating viral noncoding RNAs.
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138
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Anzelon TA, Chowdhury S, Hughes SM, Xiao Y, Lander GC, MacRae IJ. Structural basis for piRNA targeting. Nature 2021; 597:285-289. [PMID: 34471284 PMCID: PMC9302021 DOI: 10.1038/s41586-021-03856-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
PIWI proteins use PIWI-interacting RNAs (piRNAs) to identify and silence transposable elements and thereby maintain genome integrity between metazoan generations1. The targeting of transposable elements by PIWI has been compared to mRNA target recognition by Argonaute proteins2,3, which use microRNA (miRNA) guides, but the extent to which piRNAs resemble miRNAs is not known. Here we present cryo-electron microscopy structures of a PIWI-piRNA complex from the sponge Ephydatia fluviatilis with and without target RNAs, and a biochemical analysis of target recognition. Mirroring Argonaute, PIWI identifies targets using the piRNA seed region. However, PIWI creates a much weaker seed so that stable target association requires further piRNA-target pairing, making piRNAs less promiscuous than miRNAs. Beyond the seed, the structure of PIWI facilitates piRNA-target pairing in a manner that is tolerant of mismatches, leading to long-lived PIWI-piRNA-target interactions that may accumulate on transposable-element transcripts. PIWI ensures targeting fidelity by physically blocking the propagation of piRNA-target interactions in the absence of faithful seed pairing, and by requiring an extended piRNA-target duplex to reach an endonucleolytically active conformation. PIWI proteins thereby minimize off-targeting cellular mRNAs while defending against evolving genomic threats.
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Affiliation(s)
- Todd A Anzelon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Saikat Chowdhury
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Siobhan M Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel C Lander
- 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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139
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La Rocca G, King B, Shui B, Li X, Zhang M, Akat KM, Ogrodowski P, Mastroleo C, Chen K, Cavalieri V, Ma Y, Anelli V, Betel D, Vidigal J, Tuschl T, Meister G, Thompson CB, Lindsten T, Haigis K, Ventura A. Inducible and reversible inhibition of miRNA-mediated gene repression in vivo. eLife 2021; 10:e70948. [PMID: 34463618 PMCID: PMC8476124 DOI: 10.7554/elife.70948] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022] Open
Abstract
Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss-of-function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.
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Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Xiaoyi Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kemal M Akat
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Yilun Ma
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, United States
| | - Viviana Anelli
- Center of Integrative Biology, University of Trento, Trento, Italy
| | - Doron Betel
- Hem/Oncology, Medicine and Institution for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Joana Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Gunter Meister
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Tullia Lindsten
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
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140
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MiRNAs and Cancer: Key Link in Diagnosis and Therapy. Genes (Basel) 2021; 12:genes12081289. [PMID: 34440464 PMCID: PMC8395027 DOI: 10.3390/genes12081289] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of the first microRNA (miRNA), the exploration of miRNA biology has come to a new era in recent decades. Monumental studies have proven that miRNAs can be dysregulated in different types of cancers and the roles of miRNAs turn out to function to either tumor promoters or tumor suppressors. The interplay between miRNAs and the development of cancers has grabbed attention of miRNAs as novel tools and targets for therapeutic attempts. Moreover, the development of miRNA delivery system accelerates miRNA preclinical implications. In this review, we depict recent advances of miRNAs in cancer and discuss the potential diagnostic or therapeutic approaches of miRNAs.
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141
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miR-122-based therapies select for three distinct resistance mechanisms based on alterations in RNA structure. Proc Natl Acad Sci U S A 2021; 118:2103671118. [PMID: 34385308 PMCID: PMC8379925 DOI: 10.1073/pnas.2103671118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
MicroRNA (miRNA)–based drugs are quickly taking the clinic by storm. Herein, we analyzed resistance-associated variants (RAVs) to the first miRNA inhibitors to make it to the clinic, namely miR-122 inhibitors for chronic hepatitis C virus (HCV) infection. We uncovered three distinct resistance mechanisms based on unique alterations to the structure of the viral RNA. Specifically, RAVs altered the structure of the viral RNA in a manner that promotes riboswitch activity, genome stability, or positive-strand viral RNA synthesis. Our findings support recent models of miR-122–mediated HCV RNA accumulation and provide mechanism(s) of resistance to antiviral therapy. These early insights into the mechanism(s) of resistance to miRNA-based therapies may be of importance as more miRNA-targeted therapies enter into the clinic. Hepatitis C virus (HCV) is a positive-sense RNA virus that interacts with a liver-specific microRNA called miR-122. miR-122 binds to two sites in the 5′ untranslated region of the viral genome and promotes HCV RNA accumulation. This interaction is important for viral RNA accumulation in cell culture, and miR-122 inhibitors have been shown to be effective at reducing viral titers in chronic HCV-infected patients. Herein, we analyzed resistance-associated variants that were isolated in cell culture or from patients who underwent miR-122 inhibitor–based therapy and discovered three distinct resistance mechanisms all based on changes to the structure of the viral RNA. Specifically, resistance-associated variants promoted riboswitch activity, genome stability, or positive-strand viral RNA synthesis, all in the absence of miR-122. Taken together, these findings provide insight into the mechanism(s) of miR-122–mediated viral RNA accumulation and provide mechanisms of antiviral resistance mediated by changes in RNA structure.
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142
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Synthesis, characterization, and miRNA-mediated PI3K suppressing activity of novel cisplatin-derived complexes of selenones. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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143
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Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex. Nat Commun 2021; 12:4061. [PMID: 34210982 PMCID: PMC8249470 DOI: 10.1038/s41467-021-24351-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/10/2021] [Indexed: 11/08/2022] Open
Abstract
PIWI proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two PIWI proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimper uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal that post-translational modifications in unstructured regions of PIWI proteins and their binding by Tudor domains that are capable of discriminating between modification states is essential for piRNA biogenesis and silencing.
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144
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Santovito D, Egea V, Bidzhekov K, Natarelli L, Mourão A, Blanchet X, Wichapong K, Aslani M, Brunßen C, Horckmans M, Hristov M, Geerlof A, Lutgens E, Daemen MJAP, Hackeng T, Ries C, Chavakis T, Morawietz H, Naumann R, von Hundelshausen P, Steffens S, Duchêne J, Megens RTA, Sattler M, Weber C. Noncanonical inhibition of caspase-3 by a nuclear microRNA confers endothelial protection by autophagy in atherosclerosis. Sci Transl Med 2021; 12:12/546/eaaz2294. [PMID: 32493793 DOI: 10.1126/scitranslmed.aaz2294] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 04/02/2020] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are versatile regulators of gene expression with profound implications for human disease including atherosclerosis, but whether they can exert posttranslational functions to control cell adaptation and whether such noncanonical features harbor pathophysiological relevance is unknown. Here, we show that miR-126-5p sustains endothelial integrity in the context of high shear stress and autophagy. Bound to argonaute-2 (Ago2), miR-126-5p forms a complex with Mex3a, which occurs on the surface of autophagic vesicles and guides its transport into the nucleus. Mutational studies and biophysical measurements demonstrate that Mex3a binds to the central U- and G-rich regions of miR-126-5p with nanomolar affinity via its two K homology domains. In the nucleus, miR-126-5p dissociates from Ago2 and binds to caspase-3 in an aptamer-like fashion with its seed sequence, preventing dimerization of the caspase and inhibiting its activity to limit apoptosis. The antiapoptotic effect of miR-126-5p outside of the RNA-induced silencing complex is important for endothelial integrity under conditions of high shear stress promoting autophagy: ablation of Mex3a or ATG5 in vivo attenuates nuclear import of miR-126-5p, aggravates endothelial apoptosis, and exacerbates atherosclerosis. In human plaques, we found reduced nuclear miR-126-5p and active caspase-3 in areas of disturbed flow. The direct inhibition of caspase-3 by nuclear miR-126-5p reveals a noncanonical mechanism by which miRNAs can modulate protein function.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Virginia Egea
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kiril Bidzhekov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - André Mourão
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Xavier Blanchet
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Coy Brunßen
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Michael Horckmans
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles (ULB), B-1070 Brussels, Belgium
| | - Michael Hristov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Arie Geerlof
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Mat J A P Daemen
- Department of Medical Biochemistry and Pathology, Amsterdam University Medical Centers, Amsterdam School of Cardiovascular Sciences (ACS), 1081HZ Amsterdam, Netherlands
| | - Tilman Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Christian Ries
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Triantafyllos Chavakis
- Institute of Clinical Chemistry and Laboratory Medicine, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Henning Morawietz
- Division of Vascular Endothelium and Microcirculation, Department of Medicine III, Faculty of Medicine, TU Dresden, D-01307 Dresden, Germany
| | - Ronald Naumann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Philipp von Hundelshausen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Sabine Steffens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands
| | - Michael Sattler
- Institute of Structural Biolology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department of Chemistry, Technical University of Munich, D-85747 Garching, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU) München, D-80336 Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, D-80336 Munich, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229HX Maastricht, Netherlands.,Munich Cluster for Systems Neurology (SyNergy), D-81377 Munich, Germany
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145
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Jiao K, Yan Q, Guo L, Qu Z, Cao S, Chen X, Li Q, Zhu Y, Li J, Wang L, Fan C, Wang F. Poly‐Adenine‐Based Spherical Nucleic Acids for Efficient Live‐Cell MicroRNA Capture. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kai Jiao
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qinglong Yan
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Linjie Guo
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Shuting Cao
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoliang Chen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Ying Zhu
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory The Interdisciplinary Research Center Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory The Interdisciplinary Research Center Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Lihua Wang
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory The Interdisciplinary Research Center Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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146
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Ben Or G, Veksler-Lublinsky I. Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. BMC Bioinformatics 2021; 22:264. [PMID: 34030625 PMCID: PMC8146624 DOI: 10.1186/s12859-021-04164-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Due to the technical challenges involved in the application of high-throughput experimental methods, datasets of direct bona fide miRNA targets exist only for a few model organisms. Machine learning (ML)-based target prediction models were successfully trained and tested on some of these datasets. There is a need to further apply the trained models to organisms in which experimental training data are unavailable. However, it is largely unknown how the features of miRNA-target interactions evolve and whether some features have remained fixed during evolution, raising questions regarding the general, cross-species applicability of currently available ML methods. RESULTS We examined the evolution of miRNA-target interaction rules and used data science and ML approaches to investigate whether these rules are transferable between species. We analyzed eight datasets of direct miRNA-target interactions in four species (human, mouse, worm, cattle). Using ML classifiers, we achieved high accuracy for intra-dataset classification and found that the most influential features of all datasets overlap significantly. To explore the relationships between datasets, we measured the divergence of their miRNA seed sequences and evaluated the performance of cross-dataset classification. We found that both measures coincide with the evolutionary distance between the compared species. CONCLUSIONS The transferability of miRNA-targeting rules between species depends on several factors, the most associated factors being the composition of seed families and evolutionary distance. Furthermore, our feature-importance results suggest that some miRNA-target features have evolved while others remained fixed during the evolution of the species. Our findings lay the foundation for the future development of target prediction tools that could be applied to "non-model" organisms for which minimal experimental data are available. AVAILABILITY AND IMPLEMENTATION The code is freely available at https://github.com/gbenor/TPVOD .
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Affiliation(s)
- Gilad Ben Or
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
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147
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Jiao K, Yan Q, Guo L, Qu Z, Cao S, Chen X, Li Q, Zhu Y, Li J, Wang L, Fan C, Wang F. Poly-Adenine-Based Spherical Nucleic Acids for Efficient Live-Cell MicroRNA Capture. Angew Chem Int Ed Engl 2021; 60:14438-14445. [PMID: 33851770 DOI: 10.1002/anie.202017039] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/27/2021] [Indexed: 11/11/2022]
Abstract
Direct delivery of exogenous non-coding nucleic acids into living cells has attracted intense interest in biological applications. However, the cell entry efficiency and target capture ability remain to be improved. Herein, we report a method for compartmenting the nucleic acids on the surface of poly-adenine-based spherical nucleic acids (polyA-SNAs) for efficient capture of oncogenic microRNAs (miRNAs) in living cells. We find that polyA-SNAs exhibit high cell entry efficiency, which is insensitive to the configuration of the anti-miRNA sequences. By programming the length of polyAs, we precisely engineered the spatial configuration of the anti-miRNA sequences in polyA-SNAs. Compartmentalized polyA-SNAs bind to miRNAs with improved capture ability as compared to densely compacted SNAs. We further demonstrate that polyA-SNAs serve as high-efficacy miRNA sponges for capturing oncogenic miRNAs both in living cells and in mice. The efficient inhibition of miRNAs results in significant suppression of tumor growth.
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Affiliation(s)
- Kai Jiao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinglong Yan
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linjie Guo
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoliang Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Lihua Wang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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148
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Hang J, Wei F, Yan Z, Zhang X, Xu K, Zhu Y. The value of miR-510 in the prognosis and development of colon cancer. Open Med (Wars) 2021; 16:795-804. [PMID: 34036176 PMCID: PMC8126670 DOI: 10.1515/med-2021-0251] [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: 06/09/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/02/2022] Open
Abstract
Purpose Colon cancer is one of the malignant tumors that threatens human health. miR-510 was demonstrated to play roles in the progression of various cancers; its dysregulation was speculated to be associated with the development of colon cancer. Methods One hundred and thirteen colon cancer patients participated in this research. With the help of RT-qPCR, the expression of miR-510 in collected tissues and cultured cells was analyzed. The association between miR-510 expression level and clinical features and prognosis of patients was evaluated. Moreover, the effects of miR-510 on cell proliferation, migration, and invasion of colon cancer were assessed by CCK8 and Transwell assay. Results miR-510 significantly upregulated in colon cancer tissues and cell lines relative to the adjacent normal tissues and colonic cells. The expression of miR-510 was significantly associated with the TNM stage and poor prognosis of patients, indicating miR-510 was involved in the disease progression and clinical prognosis of colon cancer. Additionally, the upregulation of miR-510 significantly promoted cell proliferation, migration, and invasion of colon cancer, while its knockdown significantly inhibited these cellular processes. SRCIN 1 was the direct target of miR-510 during its promoted effect on the development of colon cancer. Conclusion The upregulation of miR-510 acts as an independent prognostic indicator and a tumor promoter by targeting SRCIN 1 in colon cancer, which provides novel therapeutic strategies for colon cancer.
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Affiliation(s)
- Junjie Hang
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
| | - Feifei Wei
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
| | - Zhiying Yan
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
| | - Xianming Zhang
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
| | - Kequn Xu
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
| | - Yingwei Zhu
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, 213003, People's Republic of China
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149
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 PMCID: PMC8130916 DOI: 10.1371/journal.ppat.1009217] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response. Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular miRNA targets and the relative abundance of each miRNA-mRNA interaction. We also show that viral miRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular miRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (ST); (EKF)
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
- * E-mail: (ST); (EKF)
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150
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Sinnett SE, Boyle E, Lyons C, Gray SJ. Engineered microRNA-based regulatory element permits safe high-dose miniMECP2 gene therapy in Rett mice. Brain 2021; 144:3005-3019. [PMID: 33950254 DOI: 10.1093/brain/awab182] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/12/2022] Open
Abstract
MECP2 gene transfer has been shown to extend the survival of Mecp2-/y knockout (KO) mice modeling Rett syndrome (RTT), an X-linked neurodevelopmental disorder. However, controlling deleterious overexpression of MeCP2 remains the critical unmet obstacle towards a safe and effective gene therapy approach for RTT. A recently developed truncated miniMECP2 gene has also been shown to be therapeutic after AAV9-mediated gene transfer in KO neonates. We show that AAV9/miniMECP2 has a similar dose-dependent toxicity profile to that of a published second-generation AAV9/MECP2 vector after treatment in adolescent mice. To overcome that toxicity, we developed a risk-driven viral genome design strategy rooted in high-throughput profiling and genome mining to rationally develop a compact, synthetic miRNA target panel (miR-Responsive Auto-Regulatory Element, "miRARE") to minimize the possibility of miniMECP2 transgene overexpression in the context of RTT gene therapy. The goal of miRARE is to have a built-in inhibitory element responsive to MeCP2 overexpression. The data provided herein show that insertion of miRARE into the miniMECP2 gene expression cassette greatly improved the safety of miniMECP2 gene transfer without compromising efficacy. Importantly, this built-in regulation system does not require any additional exogenous drug application, and no miRNAs are expressed from the transgene cassette. Although broad applications of miRARE have yet to be determined, the design of miRARE suggests a potential use in gene therapy approaches for other dose-sensitive genes.
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Affiliation(s)
- Sarah E Sinnett
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Emily Boyle
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Christopher Lyons
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Steven J Gray
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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