101
|
Li F, Tan W, Chen H, Zhou J, Xu M, Yuan G. Up- and downregulation of mature miR-1587 function by modulating its G-quadruplex structure and using small molecules. Int J Biol Macromol 2018; 121:127-134. [PMID: 30290263 DOI: 10.1016/j.ijbiomac.2018.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022]
Abstract
Using bioinformatics analysis, we found some mature human miRNAs containing G-rich sequences with four G-tracts that had a high probability of forming G-quadruplex structures. Here, we chose G-rich miR-1587 as a model to characterize the function and regulation of miRNAs. Using electrospray ionization mass spectrometry, magnetic resonance imaging, circular dichroism spectrometry, we had confirmed that miR-1587 folded into a stable parallel G-quadruplex structure. By microarray, Q-RT-PCR and 3'UTR luciferase assay, TAGLN, an early marker of smooth muscle differentiation and tumor suppressor, was identified as a target gene of miR-1587, thus providing a direct target to study miR-1587 functions. We identified three aspects of miR-1587 regulation: 1) KCl induced miR-1587 G-quadruplex formation, reducing the interaction between miR-1587 and the target gene, and inhibiting miR-1587 function; 2) pseudopalmatine ligand further inhibited miR-1587 binding to TAGLN mRNA, which disrupted its function and increased the TAGLN expression; 3) the addition of TMPyP4 ligand interfered G-quadruplex formation, and significantly enhanced miR-1587 regulation of TAGLN expression. This study has revealed the possibility of using the G-quadruplex structure as a strategy to regulate miR-1587 function, showing potential for the development of up- and downregulation of mature G-rich microRNA function by modulating its G-quadruplex and using small molecules.
Collapse
Affiliation(s)
- Fangyuan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Han Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Ming Xu
- Institute of Vascular Medicine, Department of Cardiology, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health Beijing, 100191, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
102
|
Marchand A, Rosu F, Zenobi R, Gabelica V. Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry. J Am Chem Soc 2018; 140:12553-12565. [PMID: 30183275 DOI: 10.1021/jacs.8b07302] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Designing ligands targeting G-quadruplex nucleic acid structures and affecting cellular processes is complicated because there are multiple target sequences and some are polymorphic. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry enables one to detect and quantify each specific stoichiometry (number of strands, cations, and ligands) and thus to simultaneously determine the equilibrium constants for each complex. Using a temperature-controlled nanoelectrospray source, we determined the temperature dependence of the equilibrium constants, and thus the enthalpic and entropic contributions to the formation of each stoichiometry. Enthalpy drives the formation of each quartet-K+-quartet unit, whereas entropy drives the formation of quartet-K+-triplet units. Consequently, slip-stranded structures can become more abundant as the temperature increases. In the presence of ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy), we observed that, even when only a 1:1 (ligand/quadruplex) complex is observed at room temperature, new states are populated at intermediate temperatures, including 2:1 complexes. In most cases, ligand-G4-quadruplex binding is entropically driven, and we discuss that this may have resulted from biases when ranking ligand potency using melting experiments. Other thermodynamic profiles could be linked to topology changes in terms of number of G-quartets (reflected in the number of specific K+ ions in the complex). The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and topology changes in terms of number of G-quartets.
Collapse
Affiliation(s)
- Adrien Marchand
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Frédéric Rosu
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Valérie Gabelica
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
| |
Collapse
|
103
|
Tian T, Chen YQ, Wang SR, Zhou X. G-Quadruplex: A Regulator of Gene Expression and Its Chemical Targeting. Chem 2018. [DOI: 10.1016/j.chempr.2018.02.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
104
|
Gendron TF, Petrucelli L. Disease Mechanisms of C9ORF72 Repeat Expansions. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a024224. [PMID: 28130314 DOI: 10.1101/cshperspect.a024224] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
G4C2 repeat expansions within the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). These bidirectionally transcribed expansions lead to (1) the accumulation of sense G4C2 and antisense G2C4 repeat-containing RNA, (2) the production of proteins of repeating dipeptides through unconventional translation of these transcripts, and (3) decreased C9ORF72 mRNA and protein expression. Consequently, there is ample opportunity for the C9ORF72 mutation to give rise to a spectrum of clinical manifestations, ranging from muscle weakness and atrophy to changes in behavior and cognition. It is thus somewhat surprising that investigations of these three seemingly disparate events often converge on similar putative pathological mechanisms. This review aims to summarize the findings and questions emerging from the field's quest to decipher how C9ORF72 repeat expansions cause the devastating diseases collectively referred to as "c9ALS/FTD."
Collapse
Affiliation(s)
- Tania F Gendron
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, Florida 32224
| |
Collapse
|
105
|
Zamiri B, Mirceta M, Abu-Ghazalah R, Wold MS, Pearson CE, Macgregor RB. Stress-induced acidification may contribute to formation of unusual structures in C9orf72-repeats. Biochim Biophys Acta Gen Subj 2018; 1862:1482-1491. [PMID: 29550431 DOI: 10.1016/j.bbagen.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/22/2018] [Accepted: 03/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Expansion of the C9orf72 hexanucleotide repeat (GGGGCC)n·(GGCCCC)n is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both strands of the C9orf72 repeat have been shown to form unusual DNA and RNA structures that are thought to be involved in mutagenesis and/or pathogenesis. We previously showed that the C-rich DNA strands from the C9orf72 repeat can form four-stranded quadruplexes at neutral pH. The cytosine residues become protonated under slightly acidic pH (pH 4.5-6.2), facilitating the formation of intercalated i-motif structures. METHODS Using CD spectroscopy, UV melting, and gel electrophoresis, we demonstrate a pH-induced structural transition of the C-rich DNA strand of the C9orf72 repeat at pHs reported to exist in living cells under stress, including during neurodegeneration and cancer. RESULTS We show that the repeats with lengths of 4, 6, and 8 units, form intercalated quadruplex i-motifs at low pH (pH < 5) and monomolecular hairpins and monomolecular quadruplexes under neutral-basic conditions (pH ≥ 8). Furthermore, we show that the human replication protein A (RPA) binds to the G-rich and C-rich DNA strands under acidic conditions, suggesting that it can bind to i-motif structures. CONCLUSIONS In the proper sequence context, i-motif structures can form at pH values found in some cells in vivo. GENERAL SIGNIFICANCE DNA conformational plasticity exists over broad range of solution conditions.
Collapse
Affiliation(s)
- Bita Zamiri
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mila Mirceta
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Rashid Abu-Ghazalah
- W. Booth School of Engineering Technology Practice and Technology, McMaster University, Hamilton, Ontario L8S 0A3, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
| |
Collapse
|
106
|
Moens TG, Mizielinska S, Niccoli T, Mitchell JS, Thoeng A, Ridler CE, Grönke S, Esser J, Heslegrave A, Zetterberg H, Partridge L, Isaacs AM. Sense and antisense RNA are not toxic in Drosophila models of C9orf72-associated ALS/FTD. Acta Neuropathol 2018; 135:445-457. [PMID: 29380049 PMCID: PMC6385858 DOI: 10.1007/s00401-017-1798-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
A GGGGCC hexanucleotide repeat expansion in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Neurodegeneration may occur via transcription of the repeats into inherently toxic repetitive sense and antisense RNA species, or via repeat-associated non-ATG initiated translation (RANT) of sense and antisense RNA into toxic dipeptide repeat proteins. We have previously demonstrated that regular interspersion of repeat RNA with stop codons prevents RANT (RNA-only models), allowing us to study the role of repeat RNA in isolation. Here we have created novel RNA-only Drosophila models, including the first models of antisense repeat toxicity, and flies expressing extremely large repeats, within the range observed in patients. We generated flies expressing ~ 100 repeat sense or antisense RNA either as part of a processed polyadenylated transcript or intronic sequence. We additionally created Drosophila expressing > 1000 RNA-only repeats in the sense direction. When expressed in adult Drosophila neurons polyadenylated repeat RNA is largely cytoplasmic in localisation, whilst intronic repeat RNA forms intranuclear RNA foci, as does > 1000 repeat RNA, thus allowing us to investigate both nuclear and cytoplasmic RNA toxicity. We confirmed that these RNA foci are capable of sequestering endogenous Drosophila RNA-binding proteins, and that the production of dipeptide proteins (poly-glycine–proline, and poly-glycine–arginine) is suppressed in our models. We find that neither cytoplasmic nor nuclear sense or antisense RNA are toxic when expressed in adult Drosophila neurons, suggesting they have a limited role in disease pathogenesis.
Collapse
Affiliation(s)
- Thomas G Moens
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK
| | - Sarah Mizielinska
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9RT, UK
- UK Dementia Research Institute at King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RT, UK
| | - Teresa Niccoli
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK
| | - Jamie S Mitchell
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Annora Thoeng
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Charlotte E Ridler
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Sebastian Grönke
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Jacqueline Esser
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Amanda Heslegrave
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 1PJ, UK
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Henrik Zetterberg
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 1PJ, UK
- Clinical Neurochemistry Laboratory, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, WC1N 3BG, UK
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK.
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, WC1N 3BG, UK.
- UK Dementia Research Institute at UCL, UCL Institute of Neurology, London, WC1N 3BG, UK.
| |
Collapse
|
107
|
Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD. Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chem Rev 2018; 118:1599-1663. [PMID: 29322778 DOI: 10.1021/acs.chemrev.7b00504] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.
Collapse
Affiliation(s)
- Alicia J Angelbello
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jonathan L Chen
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peiyuan Zhang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Zi-Fu Wang
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Departments of Chemistry and Neuroscience, The Scripps Research Institute , 130 Scripps Way, Jupiter, Florida 33458, United States
| |
Collapse
|
108
|
Thermodynamic and spectroscopic investigations of TMPyP4 association with guanine- and cytosine-rich DNA and RNA repeats of C9orf72. Biochem Biophys Res Commun 2018; 495:2410-2417. [DOI: 10.1016/j.bbrc.2017.12.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 02/02/2023]
|
109
|
Huang H, Zhang J, Harvey SE, Hu X, Cheng C. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes Dev 2017; 31:2296-2309. [PMID: 29269483 PMCID: PMC5769772 DOI: 10.1101/gad.305862.117] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022]
Abstract
Here, Huang et al. investigated the role of RNA secondary structure in splicing regulation and show that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in hnRNPF-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome, thus providing new insights into the regulation of alternative splicing. It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in heterogeneous nuclear ribonucleoprotein F (hnRNPF)-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an epithelial–mesenchymal transition (EMT)-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA (The Cancer Genome Atlas) data sets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.
Collapse
Affiliation(s)
- Huilin Huang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jing Zhang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Samuel E Harvey
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaohui Hu
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chonghui Cheng
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
110
|
Tang SS, Li J, Tan L, Yu JT. Genetics of Frontotemporal Lobar Degeneration: From the Bench to the Clinic. J Alzheimers Dis 2017; 52:1157-76. [PMID: 27104909 DOI: 10.3233/jad-160236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Frontotemporal lobar degeneration (FTLD) is a clinically heterogeneous neurodegenerative disease with a strong genetic component. In this review, we summarize most common mutations in MAPT, GRN, and C90RF72, as well as less common mutations in VCP, CHMP2B, TARDBP, FUS gene and so on. Several guidelines have been developed to help gene testing based on genotype-phenotype correlation, the underlying histopathological subtypes, and the neuroanatomic associations. Furthermore, we also summarize molecular pathways implicated by genes and novel targets for FTLD prevention and management in recent years.
Collapse
|
111
|
Cammas A, Millevoi S. RNA G-quadruplexes: emerging mechanisms in disease. Nucleic Acids Res 2017; 45:1584-1595. [PMID: 28013268 PMCID: PMC5389700 DOI: 10.1093/nar/gkw1280] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022] Open
Abstract
RNA G-quadruplexes (G4s) are formed by G-rich RNA sequences in protein-coding (mRNA) and non-coding (ncRNA) transcripts that fold into a four-stranded conformation. Experimental studies and bioinformatic predictions support the view that these structures are involved in different cellular functions associated to both DNA processes (telomere elongation, recombination and transcription) and RNA post-transcriptional mechanisms (including pre-mRNA processing, mRNA turnover, targeting and translation). An increasing number of different diseases have been associated with the inappropriate regulation of RNA G4s exemplifying the potential importance of these structures on human health. Here, we review the different molecular mechanisms underlying the link between RNA G4s and human diseases by proposing several overlapping models of deregulation emerging from recent research, including (i) sequestration of RNA-binding proteins, (ii) aberrant expression or localization of RNA G4-binding proteins, (iii) repeat associated non-AUG (RAN) translation, (iv) mRNA translational blockade and (v) disabling of protein–RNA G4 complexes. This review also provides a comprehensive survey of the functional RNA G4 and their mechanisms of action. Finally, we highlight future directions for research aimed at improving our understanding on RNA G4-mediated regulatory mechanisms linked to diseases.
Collapse
Affiliation(s)
- Anne Cammas
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III-Paul Sabatier, Inserm, CRCT, Toulouse, France
| | - Stefania Millevoi
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III-Paul Sabatier, Inserm, CRCT, Toulouse, France
| |
Collapse
|
112
|
Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
Collapse
|
113
|
Fay MM, Lyons SM, Ivanov P. RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms. J Mol Biol 2017; 429:2127-2147. [PMID: 28554731 PMCID: PMC5603239 DOI: 10.1016/j.jmb.2017.05.017] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/12/2017] [Accepted: 05/16/2017] [Indexed: 11/26/2022]
Abstract
G-quadruplexes (G4s) are extremely stable DNA or RNA secondary structures formed by sequences rich in guanine. These structures are implicated in many essential cellular processes, and the number of biological functions attributed to them continues to grow. While DNA G4s are well understood on structural and, to some extent, functional levels, RNA G4s and their functions have received less attention. The presence of bona fide RNA G4s in cells has long been a matter of debate. The development of G4-specific antibodies and ligands hinted on their presence in vivo, but recent advances in RNA sequencing coupled with chemical footprinting suggested the opposite. In this review, we will critically discuss the biology of RNA G4s focusing on the molecular mechanisms underlying their proposed functions.
Collapse
Affiliation(s)
- Marta M Fay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn M Lyons
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| |
Collapse
|
114
|
Kulikov K, Nozinovic S, Kath-Schorr S. The 5'-AG 5 CC-3' Fragment from the Human CPEB3 Ribozyme Forms an Ultrastable Parallel RNA G-Quadruplex. Chembiochem 2017; 18:969-973. [PMID: 28296179 DOI: 10.1002/cbic.201700028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 11/07/2022]
Abstract
An unusually thermostable G-quadruplex is formed by a sequence fragment of a naturally occurring ribozyme, the human CPEB3 ribozyme. Strong evidence is provided for the formation of a uniquely stable intermolecular G-quadruplex structure consisting of five tetrad layers, by using CD spectroscopy, UV melting curves, 2D NMR spectroscopy, and gel shift analysis. The cationic porphyrin TMPyP4 destabilizes the complex.
Collapse
Affiliation(s)
- Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Senada Nozinovic
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| |
Collapse
|
115
|
Herranz-Martin S, Chandran J, Lewis K, Mulcahy P, Higginbottom A, Walker C, Valenzuela IMPY, Jones RA, Coldicott I, Iannitti T, Akaaboune M, El-Khamisy SF, Gillingwater TH, Shaw PJ, Azzouz M. Viral delivery of C9orf72 hexanucleotide repeat expansions in mice leads to repeat-length-dependent neuropathology and behavioural deficits. Dis Model Mech 2017; 10:859-868. [PMID: 28550099 PMCID: PMC5536911 DOI: 10.1242/dmm.029892] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023] Open
Abstract
Intronic GGGGCC repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two major pathologies stemming from the hexanucleotide RNA expansions (HREs) have been identified in postmortem tissue: intracellular RNA foci and repeat-associated non-ATG dependent (RAN) dipeptides, although it is unclear how these and other hallmarks of disease contribute to the pathophysiology of neuronal injury. Here, we describe two novel lines of mice that overexpress either 10 pure or 102 interrupted GGGGCC repeats mediated by adeno-associated virus (AAV) and recapitulate the relevant human pathology and disease-related behavioural phenotypes. Similar levels of intracellular RNA foci developed in both lines of mice, but only mice expressing 102 repeats generated C9orf72 RAN pathology, neuromuscular junction (NMJ) abnormalities, dispersal of the hippocampal CA1, enhanced apoptosis, and deficits in gait and cognition. Neither line of mice, however, showed extensive TAR DNA-binding protein 43 (TDP-43) pathology or neurodegeneration. Our data suggest that RNA foci pathology is not a good predictor of C9orf72 RAN dipeptide formation, and that RAN dipeptides and NMJ dysfunction are drivers of C9orf72 disease pathogenesis. These AAV-mediated models of C9orf72-associated ALS/FTD will be useful tools for studying disease pathophysiology and developing new therapeutic approaches. Summary:C9orf72-linked motor neuron disease models with viral-mediated expression of GGGGCC repeat expansion in mice show neuropathology and behavioural deficits.
Collapse
Affiliation(s)
- Saul Herranz-Martin
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Jayanth Chandran
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Katherine Lewis
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Padraig Mulcahy
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Callum Walker
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK.,Department of Molecular Biology and Biotechnology, Krebs and Sheffield Institute for Nucleic Acids, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | | | - Ross A Jones
- Centre for Integrative Physiology & Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, The University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
| | - Ian Coldicott
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Tommaso Iannitti
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Mohammed Akaaboune
- Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Krebs and Sheffield Institute for Nucleic Acids, Firth Court, University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas H Gillingwater
- Centre for Integrative Physiology & Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, The University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - Mimoun Azzouz
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), The University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| |
Collapse
|
116
|
Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
Collapse
Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| |
Collapse
|
117
|
Zhou CQ, Liao TC, Li ZQ, Gonzalez-Garcia J, Reynolds M, Zou M, Vilar R. Dinickel-Salphen Complexes as Binders of Human Telomeric Dimeric G-Quadruplexes. Chemistry 2017; 23:4713-4722. [PMID: 28207952 PMCID: PMC5516229 DOI: 10.1002/chem.201700276] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Indexed: 12/12/2022]
Abstract
Three new polyether‐tethered dinickel–salphen complexes (2 a–c) have been synthesized and fully characterized by NMR spectroscopy, mass spectrometry, and elemental analyses. The binding affinity and selectivity of these complexes and of the parent mono‐nickel complex (1) towards dimeric quadruplex DNA have been determined by UV/Vis titrations, fluorescence spectroscopy, CD spectroscopy, and electrophoresis. These studies have shown that the dinickel–salphen complex with the longest polyether linker (2 c) has higher binding affinity and selectivity towards dimeric quadruplexes (over monomeric quadruplexes) than the dinickel–salphen complexes with the shorter polyether linkers (2 a and 2 b). Complex 2 c also has higher selectivity towards human telomeric dimeric quadruplexes with one TTA linker than the monometallic complex 1. Based on the spectroscopic data, a possible binding mode between complex 2 c and the dimeric G‐quadruplex DNA under study is proposed.
Collapse
Affiliation(s)
- Chun-Qiong Zhou
- Department of Chemistry, Imperial College London, South Kensington, London, SW72AZ, UK.,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Ting-Cong Liao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Zi-Qi Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Jorge Gonzalez-Garcia
- Department of Chemistry, Imperial College London, South Kensington, London, SW72AZ, UK
| | - Matthew Reynolds
- Department of Chemistry, Imperial College London, South Kensington, London, SW72AZ, UK
| | - Min Zou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, South Kensington, London, SW72AZ, UK
| |
Collapse
|
118
|
Koon AC, Chan HYE. Drosophila melanogaster As a Model Organism to Study RNA Toxicity of Repeat Expansion-Associated Neurodegenerative and Neuromuscular Diseases. Front Cell Neurosci 2017; 11:70. [PMID: 28377694 PMCID: PMC5359753 DOI: 10.3389/fncel.2017.00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/27/2017] [Indexed: 12/14/2022] Open
Abstract
For nearly a century, the fruit fly, Drosophila melanogaster, has proven to be a valuable tool in our understanding of fundamental biological processes, and has empowered our discoveries, particularly in the field of neuroscience. In recent years, Drosophila has emerged as a model organism for human neurodegenerative and neuromuscular disorders. In this review, we highlight a number of recent studies that utilized the Drosophila model to study repeat-expansion associated diseases (READs), such as polyglutamine diseases, fragile X-associated tremor/ataxia syndrome (FXTAS), myotonic dystrophy type 1 (DM1) and type 2 (DM2), and C9ORF72-associated amyotrophic lateral sclerosis/frontotemporal dementia (C9-ALS/FTD). Discoveries regarding the possible mechanisms of RNA toxicity will be focused here. These studies demonstrate Drosophila as an excellent in vivo model system that can reveal novel mechanistic insights into human disorders, providing the foundation for translational research and therapeutic development.
Collapse
Affiliation(s)
- Alex C Koon
- Laboratory of Drosophila ResearchHong Kong, Hong Kong; Biochemistry ProgramHong Kong, Hong Kong
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila ResearchHong Kong, Hong Kong; Biochemistry ProgramHong Kong, Hong Kong; Cell and Molecular Biology ProgramHong Kong, Hong Kong; Molecular Biotechnology Program, Faculty of Science, School of Life SciencesHong Kong, Hong Kong; School of Life Sciences, Gerald Choa Neuroscience Centre, The Chinese University of Hong KongHong Kong, Hong Kong
| |
Collapse
|
119
|
Ji AL, Zhang X, Chen WW, Huang WJ. Genetics insight into the amyotrophic lateral sclerosis/frontotemporal dementia spectrum. J Med Genet 2017; 54:145-154. [DOI: 10.1136/jmedgenet-2016-104271] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/12/2022]
|
120
|
Pandey S, Agarwala P, Maiti S. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
121
|
Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences. Sci Rep 2016; 6:39239. [PMID: 27995955 PMCID: PMC5171706 DOI: 10.1038/srep39239] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Piperine, a naturally occurring alkaloid, is well known as anti-oxidant, anti-mutagenic, anti-tumor and anti-proliferative agent. Piperine exerts such pharmacological activities by binding or interacting with various cellular targets. Recently, the first report for Piperine interaction with duplex DNA has been published last year but its interaction with G-quadruplex structures has not been studied yet. Herein, we report for the first time the interaction of Piperine with various DNA G-quadruplex structures. Comprehensive biophysical techniques were employed to determine the basis of interaction for the complex formed between Piperine and G-quadruplex DNA sequences. Piperine showed specificity for G-quadruplex DNA over double stranded DNA, with highest affinity for G-quadruplex structure formed at c-myc promoter region. Further, in-vitro studies show that Piperine causes apoptosis-mediated cell death that further emphasizes the potential of this natural product, Piperine, as a promising candidate for targeting G-quadruplex structure and thus, acts as a potent anti-cancer agent.
Collapse
|
122
|
Solomonov AV, Shipitsyna MK, Vashurin AS, Rumyantsev EV, Timin AS, Ivanov SP. Analysis of binding ability of two tetramethylpyridylporphyrins to albumin and its complex with bilirubin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 168:12-20. [PMID: 27267279 DOI: 10.1016/j.saa.2016.05.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/27/2016] [Accepted: 05/28/2016] [Indexed: 06/06/2023]
Abstract
An interaction between 5,10,15,20-tetrakis-(N-methyl-x-pyridyl)porphyrins, x=2; 4 (TMPyPs) with bovine serum albumin (BSA) and its bilirubin (BR) complex was investigated by UV-Viz and fluorescence spectroscopy under imitated physiological conditions involving molecular docking studies. The parameters of forming intermolecular complexes (binding constants, quenching rate constants, quenching sphere radius etc.) were determined. It was showed that the interaction between proteins and TMPyPs occurs via static quenching of protein fluorescence and has predominantly hydrophobic and electrostatic character. It was revealed that obtained complexes are relatively stable, but in the case of TMPyP4 binding with proteins occurs better than TMPyP2. Nevertheless, both TMPyPs have better binding ability with free protein compared to BRBSA at the same time. The influence of TMPyPs on the conformational changes in protein molecules was studied using synchronous fluorescence spectroscopy. It was found that there is no competition of BR with TMPyPs for binging sites on protein molecule and BR displacement does not occur. Molecular docking calculations have showed that TMPyPs can bind with albumin via tryptophan residue in the hydrophilic binding site of protein molecule but it is not one possible interaction way.
Collapse
Affiliation(s)
- Alexey V Solomonov
- Inorganic Chemistry Department, Ivanovo State University of Chemistry and Technology, 7 Sheremetevskij prosp., 153000 Ivanovo, Russian Federation; Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Maria K Shipitsyna
- Inorganic Chemistry Department, Ivanovo State University of Chemistry and Technology, 7 Sheremetevskij prosp., 153000 Ivanovo, Russian Federation.
| | - Arthur S Vashurin
- Inorganic Chemistry Department, Ivanovo State University of Chemistry and Technology, 7 Sheremetevskij prosp., 153000 Ivanovo, Russian Federation.
| | - Evgeniy V Rumyantsev
- Inorganic Chemistry Department, Ivanovo State University of Chemistry and Technology, 7 Sheremetevskij prosp., 153000 Ivanovo, Russian Federation.
| | - Alexander S Timin
- Inorganic Chemistry Department, Ivanovo State University of Chemistry and Technology, 7 Sheremetevskij prosp., 153000 Ivanovo, Russian Federation; Tomsk Polytechnic University, RASA Center in Tomsk, 30, Lenin Avenue, 634500 Tomsk, Russian Federation.
| | - Sergey P Ivanov
- Ufa Institute of Chemistry of the Russian Academy of Sciences, Prosp. Oktyabrya 71, Ufa 450045, Russian Federation.
| |
Collapse
|
123
|
Kumar V, kashav T, Islam A, Ahmad F, Hassan MI. Structural insight into C9orf72 hexanucleotide repeat expansions: Towards new therapeutic targets in FTD-ALS. Neurochem Int 2016; 100:11-20. [DOI: 10.1016/j.neuint.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
|
124
|
Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics 2016; 108:224-231. [PMID: 27789319 DOI: 10.1016/j.ygeno.2016.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022]
Abstract
The AT-rich genome of P. falciparum has uniquely localized G-rich stretches that have propensity to form G-quadruplexes. However, their global occurrence and potential biological roles in the parasite are poorly explored. Our genome-wide analysis revealed unique enrichment of quadruplexes in P. falciparum genome which was remarkably different from other Plasmodium species. A distinct predominance of quadruplexes was observed in nuclear and organellar genes that participate in antigenic variation, pathogenesis, DNA/RNA regulation, metabolic and protein quality control processes. Data also suggested association of quadruplexes with SNPs and DNA methylation. Furthermore, analysis of steady state mRNA (RNA-seq) and polysome-associated mRNA (Ribosome profiling) data revealed stage-specific differences in translational efficiency of quadruplex harboring genes. Taken together, our findings hint towards existence of regulatory dynamics associated with quadruplexes that may modulate translational efficiency of quadruplex harboring genes to provide survival advantage to the parasite against host immune response and antimalarial drug pressure.
Collapse
Affiliation(s)
- Deeksha Bhartiya
- ICMR-Institute of Cytology and Preventive Oncology, Noida 201301, Uttar Pradesh, India
| | - Vandna Chawla
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India
| | - Sourav Ghosh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India
| | - Ravi Shankar
- CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
| |
Collapse
|
125
|
Conlon EG, Lu L, Sharma A, Yamazaki T, Tang T, Shneider NA, Manley JL. The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains. eLife 2016; 5. [PMID: 27623008 PMCID: PMC5050020 DOI: 10.7554/elife.17820] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022] Open
Abstract
An expanded GGGGCC hexanucleotide in C9ORF72 (C9) is the most frequent known cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). It has been proposed that expanded transcripts adopt G-quadruplex (G-Q) structures and associate with proteins, but whether this occurs and contributes to disease is unknown. Here we show first that the protein that predominantly associates with GGGGCC repeat RNA in vitro is the splicing factor hnRNP H, and that this interaction is linked to G-Q formation. We then show that G-Q RNA foci are more abundant in C9 ALS patient fibroblasts and astrocytes compared to those without the expansion, and more frequently colocalize with hnRNP H. Importantly, we demonstrate dysregulated splicing of multiple known hnRNP H-target transcripts in C9 patient brains, which correlates with elevated insoluble hnRNP H/G-Q aggregates. Together, our data implicate C9 expansion-mediated sequestration of hnRNP H as a significant contributor to neurodegeneration in C9 ALS/FTD. DOI:http://dx.doi.org/10.7554/eLife.17820.001
Collapse
Affiliation(s)
- Erin G Conlon
- Department of Biological Sciences, Columbia University, New York, United States
| | - Lei Lu
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Aarti Sharma
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, United States
| | - Timothy Tang
- Department of Biological Sciences, Columbia University, New York, United States
| | - Neil A Shneider
- Department of Neurology, Columbia University Medical Center, New York, United States
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, United States
| |
Collapse
|
126
|
Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ. Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. Nucleic Acids Res 2016; 44:9050-9070. [PMID: 27625393 PMCID: PMC5100574 DOI: 10.1093/nar/gkw803] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases.
Collapse
Affiliation(s)
- Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Bilinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
127
|
Mis MSC, Brajkovic S, Tafuri F, Bresolin N, Comi GP, Corti S. Development of Therapeutics for C9ORF72 ALS/FTD-Related Disorders. Mol Neurobiol 2016; 54:4466-4476. [PMID: 27349438 DOI: 10.1007/s12035-016-9993-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022]
Abstract
The identification of the hexanucleotide repeat expansion (HRE) GGGGCC (G4C2) in the non-coding region of the C9ORF72 gene as the most frequent genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) has opened the path for advances in the knowledge and treatment of these disorders, which remain incurable. Recent evidence suggests that HRE RNA can cause gain-of-function neurotoxicity, but haploinsufficiency has also been hypothesized. In this review, we describe the recent developments in therapeutic targeting of the pathological expansion of C9ORF72 for ALS, FTD, and other neurodegenerative disorders. Three approaches are prominent: (1) an antisense oligonucleotides/RNA interference strategy; (2) using small compounds to counteract the toxic effects directly exerted by RNA derived from the repeat transcription (foci), by the translation of dipeptide repeat proteins (DPRs) from the repeated sequence, or by the sequestration of RNA-binding proteins from the C9ORF72 expansion; and (3) gene therapy, not only for silencing the toxic RNA/protein, but also for rescuing haploinsufficiency caused by the reduced transcription of the C9ORF72 coding sequence or by the diminished availability of RNA-binding proteins that are sequestered by RNA foci. Finally, with the perspective of clinical therapy, we discuss the most promising progress that has been achieved to date in the field.
Collapse
Affiliation(s)
- Maria Sara Cipolat Mis
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Simona Brajkovic
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Francesco Tafuri
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Nereo Bresolin
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Giacomo P Comi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
| |
Collapse
|
128
|
The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease. Nat Rev Neurosci 2016; 17:383-95. [PMID: 27150398 DOI: 10.1038/nrn.2016.38] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A nucleotide repeat expansion (NRE) within the chromosome 9 open reading frame 72 (C9orf72) gene was the first of this type of mutation to be linked to multiple neurological conditions, including amyotrophic lateral sclerosis and frontotemporal dementia. The pathogenic mechanisms through which the C9orf72 NRE contributes to these disorders include loss of C9orf72 function and gain-of-function mechanisms of C9orf72 driven by toxic RNA and protein species encoded by the NRE. These mechanisms have been linked to several cellular defects - including nucleocytoplasmic trafficking deficits and nuclear stress - that have been observed in both patients and animal models.
Collapse
|
129
|
Kaulage M, Maji B, Bhat J, Iwasaki Y, Chatterjee S, Bhattacharya S, Muniyappa K. Discovery and Structural Characterization of G-quadruplex DNA in Human Acetyl-CoA Carboxylase Gene Promoters: Its Role in Transcriptional Regulation and as a Therapeutic Target for Human Disease. J Med Chem 2016; 59:5035-50. [PMID: 27058681 DOI: 10.1021/acs.jmedchem.6b00453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Accumulating evidence suggests that G-quadruplexes play vital roles in gene expression, DNA replication, and recombination. Three distinct promoters (PI, PII, and PIII) regulate human acetyl-CoA carboxylase 1 (ACC1) gene expression. In this study, we asked whether the G-rich sequences within the human ACC1 (PI and PII) promoters can form G-quadruplex structures and regulate normal DNA transactions. Using multiple complementary methods, we show that G-rich sequences of PI and PII promoters form intramolecular G-quadruplex structures and then establish unambiguously the topologies of these structures. Importantly, G-quadruplex formation in ACC1 gene promoter region blocks DNA replication and suppresses transcription, and this effect was further augmented by G-quadruplex stabilizing ligands. Altogether, these results are consistent with the notion that G-quadruplex structures exist within the human ACC1 gene promoter region, whose activity can be suppressed by G-quadruplex stabilizing ligands, thereby revealing a novel regulatory mechanism of ACC1 gene expression and as a possible therapeutic target.
Collapse
Affiliation(s)
| | | | - Jyotsna Bhat
- Department of Biophysics, Bose Institute , Kolkata 700054, India
| | - Yasumasa Iwasaki
- Department of Endocrinology, Metabolism, and Nephrology, Kochi Medical School, Kochi University , Nankoku 780-8520, Japan
| | | | | | | |
Collapse
|
130
|
Li Y, Syed J, Suzuki Y, Asamitsu S, Shioda N, Wada T, Sugiyama H. Effect of ATRX and G-Quadruplex Formation by the VNTR Sequence on α-Globin Gene Expression. Chembiochem 2016; 17:928-35. [DOI: 10.1002/cbic.201500655] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Yue Li
- Department of Chemistry; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
| | - Junetha Syed
- Department of Chemistry; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
| | - Yuki Suzuki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
| | - Norifumi Shioda
- Department of Pharmacology; Graduate School of Pharmaceutical Sciences; Tohoku University; Sendai 980-8578 Japan
| | - Takahito Wada
- Department of Medical Ethics and Medical Genetics; Graduate School of Medicine; Kyoto University; Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Kyoto 606-8501 Japan
| |
Collapse
|
131
|
Rizzu P, Blauwendraat C, Heetveld S, Lynes EM, Castillo-Lizardo M, Dhingra A, Pyz E, Hobert M, Synofzik M, Simón-Sánchez J, Francescatto M, Heutink P. C9orf72 is differentially expressed in the central nervous system and myeloid cells and consistently reduced in C9orf72, MAPT and GRN mutation carriers. Acta Neuropathol Commun 2016; 4:37. [PMID: 27079381 PMCID: PMC4832459 DOI: 10.1186/s40478-016-0306-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 03/25/2016] [Indexed: 12/12/2022] Open
Abstract
A non-coding hexanucleotide repeat expansion (HRE) in C9orf72 is a common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) acting through a loss of function mechanism due to haploinsufficiency of C9orf72 or a gain of function mediated by aggregates of bidirectionally transcribed HRE-RNAs translated into di-peptide repeat (DPR) proteins. To fully understand regulation of C9orf72 expression we surveyed the C9orf72 locus using Cap Analysis of Gene Expression sequence data (CAGEseq). We observed C9orf72 was generally lowly expressed with the exception of a subset of myeloid cells, particularly CD14+ monocytes that showed up to seven fold higher expression as compared to central nervous system (CNS) and other tissues. The expression profile at the C9orf72 locus showed a complex architecture with differential expression of the transcription start sites (TSSs) for the annotated C9orf72 transcripts between myeloid and CNS tissues suggesting cell and/or tissue specific functions. We further detected novel TSSs in both the sense and antisense strand at the C9orf72 locus and confirmed their existence in brain tissues and CD14+ monocytes. Interestingly, our experiments showed a consistent decrease of C9orf72 coding transcripts not only in brain tissue and monocytes from C9orf72-HRE patients, but also in brains from MAPT and GRN mutation carriers together with an increase in antisense transcripts suggesting these could play a role in regulation of C9orf72. We found that the non-HRE related expression changes cannot be explained by promoter methylation but by the presence of the C9orf72-HRE risk haplotype and unknown functional interactions between C9orf72, MAPT and GRN.
Collapse
|
132
|
Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
Collapse
Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
| | | | | |
Collapse
|
133
|
Kumar Mishra S, Kumar A. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw002. [PMID: 26896846 PMCID: PMC4761111 DOI: 10.1093/database/baw002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL:http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php
Collapse
Affiliation(s)
- Subodh Kumar Mishra
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 452017, Madhya Pradesh, India
| | - Amit Kumar
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 452017, Madhya Pradesh, India
| |
Collapse
|
134
|
Abstract
Quadruplex-forming sequences are widely prevalent in human and other genomes, including bacterial ones. These sequences are over-represented in eukaryotic telomeres, promoters, and 5' untranslated regions. They can form quadruplex structures, which may be transient in many situations in normal cells since they can be effectively resolved by helicase action. Mutated helicases in cancer cells are unable to unwind quadruplexes, which are impediments to transcription, translation, or replication, depending on their location within a particular gene. Small molecules that can stabilize quadruplex structures augment these effects and produce cell and proliferation growth inhibition. This article surveys the chemical biology of quadruplexes. It critically examines the major classes of quadruplex-binding small molecules that have been developed to date and the various approaches to discovering selective agents. The challenges of requiring (and achieving) small-molecule targeted selectivity for a particular quadruplex are discussed in relation to the potential of these small molecules as clinically useful therapeutic agents.
Collapse
Affiliation(s)
- Stephen Neidle
- UCL School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
| |
Collapse
|
135
|
Livesey MR, Magnani D, Cleary EM, Vasistha NA, James OT, Selvaraj BT, Burr K, Story D, Shaw CE, Kind PC, Hardingham GE, Wyllie DJA, Chandran S. Maturation and electrophysiological properties of human pluripotent stem cell-derived oligodendrocytes. Stem Cells 2016; 34:1040-53. [PMID: 26763608 PMCID: PMC4840312 DOI: 10.1002/stem.2273] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/14/2015] [Accepted: 11/05/2015] [Indexed: 12/12/2022]
Abstract
Rodent‐based studies have shown that the membrane properties of oligodendrocytes play prominent roles in their physiology and shift markedly during their maturation from the oligodendrocyte precursor cell (OPC) stage. However, the conservation of these properties and maturation processes in human oligodendrocytes remains unknown, despite their dysfunction being implicated in human neurodegenerative diseases such as multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Here, we have defined the membrane properties of human oligodendrocytes derived from pluripotent stem cells as they mature from the OPC stage, and have identified strong conservation of maturation‐specific physiological characteristics reported in rodent systems. We find that as human oligodendrocytes develop and express maturation markers, they exhibit a progressive decrease in voltage‐gated sodium and potassium channels and a loss of tetrodotoxin‐sensitive spiking activity. Concomitant with this is an increase in inwardly rectifying potassium channel activity, as well as a characteristic switch in AMPA receptor composition. All these steps mirror the developmental trajectory observed in rodent systems. Oligodendrocytes derived from mutant C9ORF72‐carryng ALS patient induced pluripotent stem cells did not exhibit impairment to maturation and maintain viability with respect to control lines despite the presence of RNA foci, suggesting that maturation defects may not be a primary feature of this mutation. Thus, we have established that the development of human oligodendroglia membrane properties closely resemble those found in rodent cells and have generated a platform to enable the impact of human neurodegenerative disease‐causing mutations on oligodendrocyte maturation to be studied. Stem Cells2016;34:1040–1053
Collapse
Affiliation(s)
- Matthew R Livesey
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Dario Magnani
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Elaine M Cleary
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Navneet A Vasistha
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Owain T James
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, Karnataka, India
| | - Bhuvaneish T Selvaraj
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Burr
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David Story
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, De Crespigny Park, London, United Kingdom
| | - Peter C Kind
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, Karnataka, India
| | - Giles E Hardingham
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - David J A Wyllie
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, Karnataka, India
| | - Siddharthan Chandran
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, Karnataka, India
| |
Collapse
|
136
|
Zhou CQ, Yang JW, Dong C, Wang YM, Sun B, Chen JX, Xu YS, Chen WH. Highly selective, sensitive and fluorescent sensing of dimeric G-quadruplexes by a dimeric berberine. Org Biomol Chem 2016; 14:191-7. [DOI: 10.1039/c5ob01723h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This paper describes the highly selective, sensitive and topology-specific fluorescent sensing of dimeric G-quadruplexes by a polyether-tethered dimeric berberine.
Collapse
Affiliation(s)
- Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jian-Wei Yang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Cheng Dong
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Yong-Min Wang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Bin Sun
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ya-Shi Xu
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| |
Collapse
|
137
|
Anti-sense DNA d(GGCCCC)n expansions in C9ORF72 form i-motifs and protonated hairpins. Sci Rep 2015; 5:17944. [PMID: 26632347 PMCID: PMC4668579 DOI: 10.1038/srep17944] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022] Open
Abstract
The G4C2 hexanucleotide repeat expansion mutation (HREM) in C9ORF72, represents the most common mutation associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Three main disease mechanisms have been proposed to date: C9ORF72 haploinsufficiency, RNA toxicity, and accumulation of dipeptide repeat proteins. Pure GC content of the HREM potentially enables the formation of various non-B DNA structures such as G-quadruplexes and i-motifs. These structures are proposed to act as promoters and regulatory elements affecting replication, transcription and translation of the surrounding region. G-quadruplexes have already been shown on the G-rich sense DNA and RNA strands (G4C2)n, the structure of the anti-sense (G2C4)n strand remains unresolved. Similar C-rich sequences may, under acidic conditions, form i-motifs consisting of two parallel duplexes in a head to tail orientation held together by hemi-protonated C+-C pairs. We show that d(G2C4)n repeats do form i-motif and protonated hairpins even under near-physiological conditions. Rather than forming a DNA duplex, i-motifs persist even in the presence of the sense strand. This preferential formation of G-quadruplex and i-motif/hairpin structures over duplex DNA, may explain HREM replicational and transcriptional instability. Furthermore, i-motifs/hairpins can represent a novel pharmacological target for C9ORF72 associated ALS and FTLD.
Collapse
|
138
|
Pandey S, Agarwala P, Jayaraj GG, Gargallo R, Maiti S. The RNA Stem-Loop to G-Quadruplex Equilibrium Controls Mature MicroRNA Production inside the Cell. Biochemistry 2015; 54:7067-78. [PMID: 26554903 DOI: 10.1021/acs.biochem.5b00574] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The biological role of the existence of overlapping structures in RNA is possible yet remains very unexplored. G-Rich tracts of RNA form G-quadruplexes, while GC-rich sequences prefer stem-loop structures. The equilibrium between alternate structures within RNA may occur and influence its functionality. We tested the equilibrium between G-quadruplex and stem-loop structure in RNA and its effect on biological processes using pre-miRNA as a model system. Dicer enzyme recognizes canonical stem-loop structures in pre-miRNA to produce mature miRNAs. Deviation from stem-loop leads to deregulated mature miRNA levels, providing readout of the existence of an alternate structure per se G-quadruplex-mediated structural interference in miRNA maturation. In vitro analysis using beacon and Dicer cleavage assays indicated that mature miRNA levels depend on relative amounts of K(+) and Mg(2+) ions, suggesting an ion-dependent structural shift. Further in cellulo studies with and without TmPyP4 (RNA G-quadruplex destabilizer) demonstrated that miRNA biogenesis is modulated by G-quadruplex to stem-loop equilibrium in a subset of pre-miRNAs. Our combined analysis thus provides evidence of the formation of noncanonical G-quadruplexes in competition with canonical stem-loop structure inside the cell and its effect on miRNA maturation in a comprehensive manner.
Collapse
Affiliation(s)
- Satyaprakash Pandey
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Prachi Agarwala
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Gopal G Jayaraj
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India
| | - Raimundo Gargallo
- Solution Equilibria and Chemometrics Group, Department of Analytical Chemistry, University of Barcelona , Diagonal 645, E-08028 Barcelona, Spain
| | - Souvik Maiti
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology , Mathura Road, New Delhi 110020, India.,CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 400008, India.,Academy of Scientific and Innovative Research (AcSIR) , Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| |
Collapse
|
139
|
Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Directly lighting up RNA G-quadruplexes from test tubes to living human cells. Nucleic Acids Res 2015; 43:9575-86. [PMID: 26476445 PMCID: PMC4787783 DOI: 10.1093/nar/gkv1040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022] Open
Abstract
RNA G-quadruplexes (G4s) are one of the key components of the transcriptome that act as efficient post-transcriptional regulatory elements in living cells. To conduct further studies of the unique biological functions of RNA G4s, techniques need to be developed that can efficiently recognize RNA G4 structures under various conditions, in fixed cells and living cells, as well as in vitro. This paper presents the development of such a method, a new technique using a cyanine dye called CyT, which can detect both canonical and non-canonical RNA G4 structures from test tubes to living human cells. The ability of CyT to distinguish between G4 and nonG4 RNA offers a promising tool for future RNA G4-based biomarker discovery and potential diagnostic applications.
Collapse
Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| |
Collapse
|
140
|
Zamiri B, Mirceta M, Bomsztyk K, Macgregor RB, Pearson CE. Quadruplex formation by both G-rich and C-rich DNA strands of the C9orf72 (GGGGCC)8•(GGCCCC)8 repeat: effect of CpG methylation. Nucleic Acids Res 2015; 43:10055-64. [PMID: 26432832 PMCID: PMC4787773 DOI: 10.1093/nar/gkv1008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022] Open
Abstract
Unusual DNA/RNA structures of the C9orf72 repeat may participate in repeat expansions or pathogenesis of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded repeats are CpG methylated with unknown consequences. Typically, quadruplex structures form by G-rich but not complementary C-rich strands. Using CD, UV and electrophoresis, we characterized the structures formed by (GGGGCC)8 and (GGCCCC)8 strands with and without 5-methylcytosine (5mCpG) or 5-hydroxymethylcytosine (5hmCpG) methylation. All strands formed heterogenous mixtures of structures, with features of quadruplexes (at pH 7.5, in K(+), Na(+) or Li(+)), but no feature typical of i-motifs. C-rich strands formed quadruplexes, likely stabilized by G•C•G•C-tetrads and C•C•C•C-tetrads. Unlike G•G•G•G-tetrads, some G•C•G•C-tetrad conformations do not require the N7-Guanine position, hence C9orf72 quadruplexes still formed when N7-deazaGuanine replace all Guanines. 5mCpG and 5hmCpG increased and decreased the thermal stability of these structures. hnRNPK, through band-shift analysis, bound C-rich but not G-rich strands, with a binding preference of unmethylated > 5hmCpG > 5mCpG, where methylated DNA-protein complexes were retained in the wells, distinct from unmethylated complexes. Our findings suggest that for C-rich sequences interspersed with G-residues, one must consider quadruplex formation and that methylation of quadruplexes may affect epigenetic processes.
Collapse
Affiliation(s)
- Bita Zamiri
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mila Mirceta
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle WA 98109, USA
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| |
Collapse
|
141
|
Zhang YQ, Zhang YH, Xie J, Li MN, Liu ZR, Shen JY, Shi SS, Lan XY, Wang S, Cheng NL. TMPyP4-regulated cell proliferation and apoptosis through the Wnt/β-catenin signaling pathway in SW480 cells. J Recept Signal Transduct Res 2015; 36:167-72. [PMID: 26382555 DOI: 10.3109/10799893.2015.1069846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND The aim of this study was to investigate the potential effects of the 5, 10, 15, 20-tetrakis (1-methylpyridinium-4-yl) porphyrin (TMPyP4) on the proliferation and apoptosis of SW480 cells and the underlying mechanisms by which TMPyP4 exerted its actions. METHODS After treated with different doses of TMPyP4, cell viability was determined by MTT method, the apoptosis was observed by flow cytometry (FCM) and the expression of Wnt, GSK-3β, β-catenin and cyclinD1 was measured by RT-PCR and Western blot analysis. RESULTS The analysis revealed that TMPyP4 potently suppressed cell viability and induced the apoptosis of SW480 cells in a dose-dependent manner. In addition, the downregulation of Wnt, β-catenin and cyclinD1 expression levels was detected in TMPyP4-treated SW480 cells. However, followed by the block of Wnt signaling pathway using siRNA methods, the effects of TMPyP4 on proliferation and apoptosis of SW480 cells were significantly reduced. CONCLUSION It indicates that the TMPyP4-inhibited proliferation and -induced apoptosis in SW480 cells was accompanied by the suppression of Wnt/β-catenin signaling pathway. Therefore, TMPyP4 may represent a potential therapeutic method for the treatment of colon carcinoma.
Collapse
Affiliation(s)
- Yi-Qiang Zhang
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China .,b Department of Biochemistry & Molecular Biology Full Affiliation , Changzhi Medical College , Changzhi , PR China , and
| | - Yue-Hong Zhang
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Jun Xie
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Mei-Ning Li
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Zhi-Rong Liu
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Jin-Yan Shen
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Shuai-Shuai Shi
- c Department of Nephrology , Changzhi Medical College Affiliated Heji Hospital , Changzhi , PR China
| | - Xiao-Yu Lan
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Shuang Wang
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| | - Niu-Liang Cheng
- a Department of Biochemistry & Molecular Biology Full Affiliation , Shanxi Medical University , Taiyuan , PR China
| |
Collapse
|
142
|
The C9orf72 repeat expansion disrupts nucleocytoplasmic transport. Nature 2015; 525:56-61. [PMID: 26308891 DOI: 10.1038/nature14973] [Citation(s) in RCA: 726] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
The hexanucleotide repeat expansion (HRE) GGGGCC (G4C2) in C9orf72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies support an HRE RNA gain-of-function mechanism of neurotoxicity, and we previously identified protein interactors for the G4C2 RNA including RanGAP1. A candidate-based genetic screen in Drosophila expressing 30 G4C2 repeats identified RanGAP (Drosophila orthologue of human RanGAP1), a key regulator of nucleocytoplasmic transport, as a potent suppressor of neurodegeneration. Enhancing nuclear import or suppressing nuclear export of proteins also suppresses neurodegeneration. RanGAP physically interacts with HRE RNA and is mislocalized in HRE-expressing flies, neurons from C9orf72 ALS patient-derived induced pluripotent stem cells (iPSC-derived neurons), and in C9orf72 ALS patient brain tissue. Nuclear import is impaired as a result of HRE expression in the fly model and in C9orf72 iPSC-derived neurons, and these deficits are rescued by small molecules and antisense oligonucleotides targeting the HRE G-quadruplexes. Nucleocytoplasmic transport defects may be a fundamental pathway for ALS and FTD that is amenable to pharmacotherapeutic intervention.
Collapse
|
143
|
DeLoach A, Cozart M, Kiaei A, Kiaei M. A retrospective review of the progress in amyotrophic lateral sclerosis drug discovery over the last decade and a look at the latest strategies. Expert Opin Drug Discov 2015; 10:1099-118. [PMID: 26307158 DOI: 10.1517/17460441.2015.1067197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Drug discovery for amyotrophic lateral sclerosis (ALS) has experienced a surge in clinical studies and remarkable preclinical milestones utilizing a variety of mutant superoxide dismutase 1 model systems. Of the drugs that were tested and showed positive preclinical effects, none demonstrated therapeutic benefits to ALS patients in clinical settings. AREAS COVERED This review discusses the advances made in drug discovery for ALS and highlights why drug development is proving to be so difficult. It also discusses how a closer look at both preclinical and clinical studies could uncover the reasons why these preclinical successes have yet to result in the availability of an effective drug for clinical use. EXPERT OPINION Valuable lessons from the numerous preclinical and clinical studies supply the biggest advantage in the monumental task of finding a cure for ALS. Obviously, a single design type for ALS clinical trials has not yielded success. The authors suggest a two-pronged approach that may prove essential to achieve clinical efficacy in the identification of novel targets and preclinical testing in multiple models to identify biomarkers that can function in diagnostic, predictive and prognostic roles, and changes to clinical trial design and patient recruitment criteria. The advancement of technology and invention of more powerful tools will further enhance the above. This will give rise to more sophisticated clinical trials with consideration of a range of criteria from: optimum dose, route of delivery, specific biomarkers, pharmacokinetics, pharmacodynamics and toxicology to biomarkers, timing for trial and patients' clinical status.
Collapse
Affiliation(s)
- Abigail DeLoach
- a 1 University of Arkansas for Medical Sciences, Department of Neurobiology and Developmental Sciences , Little Rock, AR 72205, USA
| | - Michael Cozart
- b 2 University of Arkansas for Medical Sciences, Department of Pharmacology and Toxicology , Little Rock, AR 72205, USA
| | - Arianna Kiaei
- a 1 University of Arkansas for Medical Sciences, Department of Neurobiology and Developmental Sciences , Little Rock, AR 72205, USA
| | - Mahmoud Kiaei
- a 1 University of Arkansas for Medical Sciences, Department of Neurobiology and Developmental Sciences , Little Rock, AR 72205, USA.,b 2 University of Arkansas for Medical Sciences, Department of Pharmacology and Toxicology , Little Rock, AR 72205, USA.,c 3 University of Arkansas for Medical Sciences, Department of Neurology , 4301 W. Markham St, 846, Little Rock, AR 72205 7199, USA
| |
Collapse
|
144
|
Donnelly CJ, Grima JC, Sattler R. Aberrant RNA homeostasis in amyotrophic lateral sclerosis: potential for new therapeutic targets? Neurodegener Dis Manag 2015; 4:417-37. [PMID: 25531686 DOI: 10.2217/nmt.14.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron degeneration. The disease pathogenesis is multifaceted in that multiple cellular and molecular pathways have been identified as contributors to the disease progression. Consequently, numerous therapeutic targets have been pursued for clinical development, unfortunately with little success. The recent discovery of mutations in RNA modulating genes such as TARDBP/TDP-43, FUS/TLS or C9ORF72 changed our understanding of neurodegenerative mechanisms in ALS and introduced the role of dysfunctional RNA processing as a significant contributor to disease pathogenesis. This article discusses the latest findings on such RNA toxicity pathways in ALS and potential novel therapeutic approaches.
Collapse
Affiliation(s)
- Christopher J Donnelly
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | |
Collapse
|
145
|
Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
Collapse
Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
146
|
Drosha inclusions are new components of dipeptide-repeat protein aggregates in FTLD-TDP and ALS C9orf72 expansion cases. J Neuropathol Exp Neurol 2015; 74:380-7. [PMID: 25756586 PMCID: PMC4362478 DOI: 10.1097/nen.0000000000000182] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Supplemental digital content is available in the text. Frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) are 2 neurodegenerative disorders that share clinical, genetic, and neuropathologic features. The presence of abnormal expansions of GGGGCC repeats (G4C2 repeats) in a noncoding region of the Chromosome 9 open reading frame 72 (C9orf72) gene is the major genetic cause of both FTLD and ALS. Transcribed G4C2 repeats can form nuclear RNA foci and recruit RNA-binding proteins, thereby inhibiting their normal function. Moreover, through a repeat-associated non-ATG translation mechanism, G4C2 repeats translation leads to dipeptide-repeat protein aggregation in the cytoplasm of neurons. Here, we identify Drosha protein as a new component of these dipeptide-repeat aggregates. In C9orf72 mutation cases of FTLD-TDP (c9FTLD-TDP) and ALS (c9ALS), but not in FTLD or ALS cases without C9orf72 mutation, Drosha is mislocalized to form neuronal cytoplasmic inclusions in the hippocampus, frontal cortex, and cerebellum. Further characterization of Drosha-positive neuronal cytoplasmic inclusions in the hippocampus, frontal cortex, and cerebellum revealed colocalization with p62 and ubiquilin-2, 2 pathognomonic signatures of c9FTLD-TDP and c9ALS cases; however, Drosha inclusions rarely colocalized with TDP-43 pathology. We conclude that Drosha may play a unique pathogenic role in the onset or progression of FTLD-TDP/ALS in patients with the C9orf72 mutation.
Collapse
|
147
|
Simone R, Fratta P, Neidle S, Parkinson GN, Isaacs AM. G-quadruplexes: Emerging roles in neurodegenerative diseases and the non-coding transcriptome. FEBS Lett 2015; 589:1653-68. [PMID: 25979174 DOI: 10.1016/j.febslet.2015.05.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 12/14/2022]
Abstract
G-rich sequences in DNA and RNA have a propensity to fold into stable secondary structures termed G-quadruplexes. G-quadruplex forming sequences are widespread throughout the human genome, within both, protein coding and non-coding genes, and regulatory regions. G-quadruplexes have been implicated in multiple cellular functions including chromatin epigenetic regulation, DNA recombination, transcriptional regulation of gene promoters and enhancers, and translation. Here we will review the evidence for the occurrence of G-quadruplexes both in vitro and in vivo; their role in neurological diseases including G-quadruplex-forming repeat expansions in the C9orf72 gene in frontotemporal dementia and amyotrophic lateral sclerosis and loss of the G-quadruplex binding protein FMRP in the intellectual disability fragile X syndrome. We also review mounting evidence that supports a role for G-quadruplexes in regulating the processing or function of a range of non-coding RNAs. Finally we will highlight current perspectives for therapeutic interventions that target G-quadruplexes.
Collapse
Affiliation(s)
- Roberto Simone
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| | - Pietro Fratta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Sobell Department of Motor Neuroscience and Movement, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
| |
Collapse
|
148
|
C9orf72 amyotrophic lateral sclerosis and frontotemporal dementia: gain or loss of function? Curr Opin Neurol 2015; 27:515-23. [PMID: 25188012 PMCID: PMC4165481 DOI: 10.1097/wco.0000000000000130] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purpose of review The molecular mechanisms that underlie chromosome 9 open reading frame 72 (C9orf72)-associated amyotrophic lateral sclerosis and frontotemporal dementia are rapidly emerging. Two potential disease mechanisms have been postulated – gain or loss of function. We provide an overview of recent advances that support or oppose gain-of-function and loss-of-function mechanisms. Recent findings Since the discovery that a noncoding repeat expansion in C9orf72 was responsible for chromosome 9-linked amyotrophic lateral sclerosis and frontotemporal dementia in 2011, a plethora of studies have investigated clinical, pathological and mechanistic aspects of the disease. Loss of function is supported by reduced levels of C9orf72 in patient brain and functional work, revealing a role of the C9orf72 protein in endocytic and autophagic pathways and motor function. Gain of function is supported by the presence in patient brain of both repeat RNA and protein aggregates. Repeat RNA aggregates termed RNA foci, a hallmark of noncoding repeat expansion diseases, have been shown to sequester proteins involved in RNA splicing, editing, nuclear export and nucleolar function. Repeat-associated non-ATG dependent translation gives rise to toxic dipeptide repeat proteins that form inclusions in patient tissue. Antisense oligonucleotides targeting C9orf72 have shown promise for combating gain-of-function toxicity. Summary Rapid progress is being made towards understanding this common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Overall, the weight of data currently sits in favour of gain of function as the most important disease mechanism, which has important implications for the development of effective and targeted therapies.
Collapse
|
149
|
Dai J, Liu ZQ, Wang XQ, Lin J, Yao PF, Huang SL, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. Discovery of Small Molecules for Up-Regulating the Translation of Antiamyloidogenic Secretase, a Disintegrin and Metalloproteinase 10 (ADAM10), by Binding to the G-Quadruplex-Forming Sequence in the 5' Untranslated Region (UTR) of Its mRNA. J Med Chem 2015; 58:3875-91. [PMID: 25822852 DOI: 10.1021/acs.jmedchem.5b00139] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Up-regulation of a disintegrin and metalloproteinase 10 (ADAM10) to prevent the formation of β-amyloid (Aβ) peptides might be a promising strategy to treat Alzheimer's disease (AD). RNA G-quadruplex motif within the 5'-UTR of the ADAM10 mRNA is an inhibitory element for ADAM10 translation. Thus, mitigation of the suppressive effect of this motif using an RNA G-quadruplex-forming G-rich sequence (QGRS) binder might be a new approach for AD therapy. Herein, a series of new methylquinolinium derivatives were synthesized and screened by surface plasmon resonance (SPR) and the dual-luciferase reporter assay. Among them, compound 24 showed selective affinity for the QGRS of ADAM10 and could strongly up-regulate the translation of it. Moreover, treatment with 24 led to a significant increase of the secretion of sAPPα, consequently decreasing the Aβ40 in cellular. These results illustrate that the interaction between the RNA QGRS and a small molecule may be a new molecular strategy to modulate the translation of ADAM10.
Collapse
Affiliation(s)
- Jie Dai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Zhen-Quan Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Xiao-Qin Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jing Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Pei-Fen Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| |
Collapse
|
150
|
Scotter EL, Chen HJ, Shaw CE. TDP-43 Proteinopathy and ALS: Insights into Disease Mechanisms and Therapeutic Targets. Neurotherapeutics 2015; 12:352-63. [PMID: 25652699 PMCID: PMC4404432 DOI: 10.1007/s13311-015-0338-x] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Therapeutic options for patients with amyotrophic lateral sclerosis (ALS) are currently limited. However, recent studies show that almost all cases of ALS, as well as tau-negative frontotemporal dementia (FTD), share a common neuropathology characterized by the deposition of TAR-DNA binding protein (TDP)-43-positive protein inclusions, offering an attractive target for the design and testing of novel therapeutics. Here we demonstrate how diverse environmental stressors linked to stress granule formation, as well as mutations in genes encoding RNA processing proteins and protein degradation adaptors, initiate ALS pathogenesis via TDP-43. We review the progressive development of TDP-43 proteinopathy from cytoplasmic mislocalization and misfolding through to macroaggregation and the addition of phosphate and ubiquitin moieties. Drawing from cellular and animal studies, we explore the feasibility of therapeutics that act at each point in pathogenesis, from mitigating genetic risk using antisense oligonucleotides to modulating TDP-43 proteinopathy itself using small molecule activators of autophagy, the ubiquitin-proteasome system, or the chaperone network. We present the case that preventing the misfolding of TDP-43 and/or enhancing its clearance represents the most important target for effectively treating ALS and frontotemporal dementia.
Collapse
Affiliation(s)
- Emma L. Scotter
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, de Crespigny Park, London, SE5 8AF UK
- Department of Pharmacology, University of Auckland, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Han-Jou Chen
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, de Crespigny Park, London, SE5 8AF UK
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, de Crespigny Park, London, SE5 8AF UK
| |
Collapse
|