51
|
Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
52
|
Platella C, Riccardi C, Montesarchio D, Roviello GN, Musumeci D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim Biophys Acta Gen Subj 2017; 1861:1429-1447. [PMID: 27865995 PMCID: PMC7117017 DOI: 10.1016/j.bbagen.2016.11.027] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules identified to recognize with high affinity specific targets including proteins, small molecules, ions, whole cells and even entire organisms, such as viruses or bacteria. They can be identified from combinatorial libraries of DNA or RNA oligonucleotides by SELEX technology, an in vitro iterative selection procedure consisting of binding (capture), partitioning and amplification steps. Remarkably, many of the aptamers selected against biologically relevant protein targets are G-rich sequences that can fold into stable G-quadruplex (G4) structures. Aiming at disseminating novel inspiring ideas within the scientific community in the field of G4-structures, the emphasis of this review is placed on: 1) recent advancements in SELEX technology for the efficient and rapid identification of new candidate aptamers (introduction of microfluidic systems and next generation sequencing); 2) recurrence of G4 structures in aptamers selected by SELEX against biologically relevant protein targets; 3) discovery of several G4-forming motifs in important regulatory regions of the human or viral genome bound by endogenous proteins, which per se can result into potential aptamers; 4) an updated overview of G4-based aptamers with therapeutic potential and 5) a discussion on the most attractive G4-based aptamers for diagnostic applications. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | | | - Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Napoli, Italy.
| |
Collapse
|
53
|
Kerkour A, Marquevielle J, Ivashchenko S, Yatsunyk LA, Mergny JL, Salgado GF. High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation. J Biol Chem 2017; 292:8082-8091. [PMID: 28330874 DOI: 10.1074/jbc.m117.781906] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression.
Collapse
Affiliation(s)
- Abdelaziz Kerkour
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Julien Marquevielle
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Stefaniia Ivashchenko
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Liliya A Yatsunyk
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and.,Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
| | - Jean-Louis Mergny
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Gilmar F Salgado
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| |
Collapse
|
54
|
Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
Collapse
Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
| | | | | |
Collapse
|
55
|
Pharmacological strategies to target oncogenic KRAS signaling in pancreatic cancer. Pharmacol Res 2017; 117:370-376. [DOI: 10.1016/j.phrs.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 02/07/2023]
|
56
|
Wen LN, Xie MX. Spectroscopic investigation of the interaction between G-quadruplex of KRAS promoter sequence and three isoquinoline alkaloids. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 171:287-296. [PMID: 27565766 DOI: 10.1016/j.saa.2016.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/02/2016] [Accepted: 08/10/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Li-Na Wen
- Medical Science & Research Center of Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, People's Republic of China
| | - Meng-Xia Xie
- Analytical & Testing Center of Beijing Normal University, Beijing 100875, People's Republic of China.
| |
Collapse
|
57
|
Zhu X, Luo W, Liang W, Tang F, Bei C, Ren Y, Qin L, Tan C, Zhang Y, Tan S. Overexpression and clinical significance of MYC-associated zinc finger protein in pancreatic carcinoma. Onco Targets Ther 2016; 9:7493-7501. [PMID: 28008270 PMCID: PMC5167488 DOI: 10.2147/ott.s124118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This study aimed to investigate the expression and clinical significance of MYC-associated zinc finger protein (MAZ) in pancreatic carcinoma (PC), and the biological functions of MAZ in PC cells. MAZ expression was detected in 57 PC tissues and 41 paired adjacent nontumor tissues by immunohistochemistry. Compared to the expression in adjacent nontumor tissues, MAZ was significantly higher expressed in PC tissues (P<0.0001). In addition, MAZ expression had a significant correlation with certain clinical characteristics of PC patients, such as age, tumor diameter, tumor number, and the serum level of CA199 (P<0.05). The survival analysis showed that the survival time of PC patients with high expression of MAZ was significantly lower than patients with low expression of MAZ (P=0.0365). After MAZ was knocked down in PANC-1 cells by RNA interference, the cells’ ability to proliferate, invade, and migrate was decreased significantly (P<0.01). Moreover, MAZ expression was found to be associated with Ki-67, a cell proliferation marker, in PC tissues, further supporting the idea that MAZ promotes PC cell proliferation. Our study clarifies an oncogenic role of MAZ in pathogenesis of PC and provides MAZ as a biomarker in the treatment and prognosis of PC.
Collapse
Affiliation(s)
- Xiaonian Zhu
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Wei Luo
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, People's Republic of China
| | - Wenjin Liang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guilin Medical University, Guilin, People's Republic of China
| | - Fen Tang
- Department of Hepatology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, People's Republic of China
| | - Chunhua Bei
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Yuan Ren
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Linyuan Qin
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Chao Tan
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Ying Zhang
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| | - Shengkui Tan
- School of Public Health, Guilin Medical University, Guilin, People's Republic of China
| |
Collapse
|
58
|
Chu PC, Kulp SK, Bekaii-Saab T, Chen CS. Targeting integrin-linked kinase to suppress oncogenic KRAS signaling in pancreatic cancer. Small GTPases 2016; 9:452-456. [PMID: 27936345 DOI: 10.1080/21541248.2016.1251383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although oncogenic KRAS represents a therapeutically relevant target in pancreatic cancer, it is deemed "non-druggable" because of the intrinsic difficulty in designing direct inhibitors of KRAS. Our recent work demonstrated a KRAS-integrin-linked kinase (ILK) regulatory feedback loop that allows pancreatic cancer cells to regulate KRAS expression and to interact with the tumor microenvironment to promote aggressive phenotype. KRAS induces E2F1-mediated transcriptional activation of ILK expression, and ILK, in turn, controls KRAS expression via hnRNPA1, which binds and destabilizes the G-quadruplex in the KRAS promoter. Moreover, ILK inhibition blocked KRAS-driven EMT and growth factor-stimulated KRAS expression. This regulatory loop, however, was not noted in KRAS mutant colorectal and lung cancer cells examined as knockdown of KRAS or ILK did not affect each other's expression, suggesting that this KRAS-ILK feedback regulation is specific for pancreatic cancer. In sum, this regulatory loop provides a strong mechanistic rationale for suppressing oncogenic KRAS signaling through targeting ILK, and this creating a potential new therapeutic strategy for pancreatic cancer.
Collapse
Affiliation(s)
- Po-Chen Chu
- a Institute of Biological Chemistry , Academia Sinica , Taipei , Taiwan
| | - Samuel K Kulp
- b Division of Medicinal Chemistry and Pharmacognosy , College of Pharmacy, The Ohio State University , Columbus , OH , USA
| | | | - Ching-Shih Chen
- a Institute of Biological Chemistry , Academia Sinica , Taipei , Taiwan.,b Division of Medicinal Chemistry and Pharmacognosy , College of Pharmacy, The Ohio State University , Columbus , OH , USA
| |
Collapse
|
59
|
Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells. Sci Rep 2016; 6:38468. [PMID: 27929127 PMCID: PMC5144097 DOI: 10.1038/srep38468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/10/2016] [Indexed: 12/28/2022] Open
Abstract
KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays.
Collapse
|
60
|
Critical role of hnRNP A1 in activating KRAS transcription in pancreatic cancer cells: A molecular mechanism involving G4 DNA. Biochim Biophys Acta Gen Subj 2016; 1861:1389-1398. [PMID: 27888145 DOI: 10.1016/j.bbagen.2016.11.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 01/31/2023]
Abstract
KRAS is one of the most mutated genes in human cancer. Its crucial role in the tumourigenesis of pancreatic ductal adenocarcinoma (PDAC) has been widely demonstrated. As this deadly cancer does not sufficiently respond to conventional chemotherapies, it is important to increase our knowledge of pancreatic cancer biology, in particular how oncogenic KRAS is regulated. The promoter of KRAS contains a GA-element composed of runs of guanines that fold into a G4 structure. This unusual DNA conformation is recognized by several nuclear proteins, including MAZ and hnRNP A1. Recent data have revealed that KRAS is interconnected to ILK and hnRNP A1 in a circuitry that enables pancreatic cancer cells to maintain an aggressive phenotype. The present review illustrates recent advances on how KRAS is regulated in pancreatic cancer cells, focusing on the formation of G4 structures in the KRAS promoter and their interaction with hnRNP A1. The newly discovered KRAS-ILK-hnRNP A1 regulatory loop is discussed, emphasizing its potential as a therapeutic target for PDAC-specific molecules. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
|
61
|
Mutsamwira S, Ainscough EW, Partridge AC, Derrick PJ, Filichev VV. G-Quadruplex Supramolecular Assemblies in Photochemical Upconversion. Chemistry 2016; 22:10376-81. [DOI: 10.1002/chem.201601353] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/04/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Saymore Mutsamwira
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| | - Eric W. Ainscough
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| | - Ashton C. Partridge
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
- Department of Physics and School of Engineering; The University of Auckland; 20 Symonds Street Auckland New Zealand
| | - Peter J. Derrick
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
- Department of Physics and School of Engineering; The University of Auckland; 20 Symonds Street Auckland New Zealand
| | - Vyacheslav V. Filichev
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| |
Collapse
|
62
|
Hároníková L, Coufal J, Kejnovská I, Jagelská EB, Fojta M, Dvořáková P, Muller P, Vojtesek B, Brázda V. IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation. PLoS One 2016; 11:e0157156. [PMID: 27280708 PMCID: PMC4900677 DOI: 10.1371/journal.pone.0157156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0–80) and in structurally identical parts of both HIN domains (aa 271–302 and aa 586–617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation.
Collapse
Affiliation(s)
- Lucia Hároníková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlarska 2, 61137, Brno, Czech Republic
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Eva B. Jagelská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Petra Dvořáková
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Petr Muller
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
- * E-mail:
| |
Collapse
|
63
|
Gouda AS, Amine MS, Pedersen EB. Synthesis of New DNA G-Quadruplex Constructs with Anthraquinone Insertions and Their Anticoagulant Activity. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
64
|
Cogoi S, Xodo LE. G4 DNA in ras genes and its potential in cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:663-74. [PMID: 26855080 DOI: 10.1016/j.bbagrm.2016.02.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/24/2016] [Accepted: 02/02/2016] [Indexed: 02/07/2023]
Abstract
It is now well established that in the human genome the canonical double helix coexists with folded G-quadruplex structures that are known to have important biological functions. In this review we summarize the current knowledge on quadruplex formation in the promoters of the ras genes that are mutated in about 30% of all human cancers. We describe the nuclear proteins that recognize these unusual DNA structures and discuss their function in transcription. We also examine the formation of G-quadruplexes in the 5'-untranslated region of the ras transcripts and conclude this review by reporting strategies that use either ras G-quadruplexes or proteins recognizing the ras G-quadruplexes as targets of anticancer small molecules.
Collapse
Affiliation(s)
- Susanna Cogoi
- Department of Medical and Biological Sciences, University of Udine, P.le Kolbe 4, 33100 Udine, Italy.
| | - Luigi E Xodo
- Department of Medical and Biological Sciences, University of Udine, P.le Kolbe 4, 33100 Udine, Italy.
| |
Collapse
|
65
|
El-Sayed AA, Pedersen EB, Khaireldin NY. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
66
|
Franz H, Greschik H, Willmann D, Ozretić L, Jilg CA, Wardelmann E, Jung M, Buettner R, Schüle R. The histone code reader SPIN1 controls RET signaling in liposarcoma. Oncotarget 2016; 6:4773-89. [PMID: 25749382 PMCID: PMC4467114 DOI: 10.18632/oncotarget.3000] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/21/2014] [Indexed: 12/20/2022] Open
Abstract
The histone code reader Spindlin1 (SPIN1) has been implicated in tumorigenesis and tumor growth, but the underlying molecular mechanisms remain poorly understood. Here, we show that reducing SPIN1 levels strongly impairs proliferation and increases apoptosis of liposarcoma cells in vitro and in xenograft mouse models. Combining signaling pathway, genome-wide chromatin binding, and transcriptome analyses, we found that SPIN1 directly enhances expression of GDNF, an activator of the RET signaling pathway, in cooperation with the transcription factor MAZ. Accordingly, knockdown of SPIN1 or MAZ results in reduced levels of GDNF and activated RET explaining diminished liposarcoma cell proliferation and survival. In line with these observations, levels of SPIN1, GDNF, activated RET, and MAZ are increased in human liposarcoma compared to normal adipose tissue or lipoma. Importantly, a mutation of SPIN1 within the reader domain interfering with chromatin binding reduces liposarcoma cell proliferation and survival. Together, our data describe a molecular mechanism for SPIN1 function in liposarcoma and suggest that targeting SPIN1 chromatin association with small molecule inhibitors may represent a novel therapeutic strategy.
Collapse
Affiliation(s)
- Henriette Franz
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Holger Greschik
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Dominica Willmann
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Luka Ozretić
- Universitätsklinikum Köln, Institut für Pathologie, Köln, Germany
| | - Cordula Annette Jilg
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany
| | - Eva Wardelmann
- Universitätsklinikum Münster, Gerhard-Domagk-Insitut für Pathologie, Münster, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, Germany
| | | | - Roland Schüle
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany.,BIOSS Centre of Biological Signaling Studies, Albert-Ludwigs-University, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, Germany
| |
Collapse
|
67
|
Aparin IO, Farzan VM, Veselova OA, Chistov AA, Podkolzin AT, Ustinov AV, Shipulin GA, Formanovsky AA, Korshun VA, Zatsepin TS. 1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. Analyst 2016; 141:1331-8. [PMID: 26738806 DOI: 10.1039/c5an01767j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An alkyl azide derivative of 1-phenylethynylpyrene (PEPy) dye was prepared and used in the functionalization of oligonucleotides via click chemistry. Spectral and photo-physical properties of the PEPy-modified oligonucleotides as a single strand, and in perfect or mismatched duplexes, have been studied. A series of PEPy-Dabcyl fluorogenic TaqMan probes were synthesized and tested in qPCR. PEPy proved to be a superior substitute for AMCA as a short wavelength fluorescent dye for qPCR probes. PEPy probes were shown to significantly reduce Cq (a fractional PCR cycle used for quantification) vs. AMCA labeled probes, thus improving on the reliability of detection. Moreover, a larger increase of fluorescence during amplification was observed in the case of PEPy probes that makes this dye very suitable for an end-point PCR technique. This study broadens the panel of fluorescent dyes suitable for the use in probes for quantitative real-time PCR.
Collapse
Affiliation(s)
- Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
68
|
Miglietta G, Gouda AS, Cogoi S, Pedersen EB, Xodo LE. Nucleic Acid Targeted Therapy: G4 Oligonucleotides Downregulate HRAS in Bladder Cancer Cells through a Decoy Mechanism. ACS Med Chem Lett 2015; 6:1179-83. [PMID: 26713101 DOI: 10.1021/acsmedchemlett.5b00315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/18/2015] [Indexed: 12/12/2022] Open
Abstract
In a previous study we have demonstrated that two neighboring G-quadruplexes, hras-1 and hras-2, located immediately upstream of the major transcription start site of HRAS, bind MAZ, a nuclear factor that activates transcription (Cogoi, S.; et al. Nucl. Acid Res. 2014, 42, 8379). For the present study we have designed G4 oligonucleotides with anthraquinone insertions and locked nucleic acids (LNA) modifications mimicking quadruplex hras-1. Luciferase, qRT-PCR, and Western blot data demonstrate that these constructs efficiently down regulate HRAS in T24 bladder cancer cells. The inhibitory efficiency of the G4 oligonucleotides correlates with their nuclease resistance in the cell environment. By chromatin immunoprecipitation we show that the association of MAZ to the HRAS promoter is strongly attenuated by the designed G4 oligonucleotides, thus suggesting that these constructs behave with a decoy mechanism.
Collapse
Affiliation(s)
- Giulia Miglietta
- Department
of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
| | - Alaa S. Gouda
- Nucleic
Acid Center, Institute of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Susanna Cogoi
- Department
of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
| | - Erik B. Pedersen
- Nucleic
Acid Center, Institute of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Luigi E. Xodo
- Department
of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy
| |
Collapse
|
69
|
Podbevšek P, Plavec J. KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units. Nucleic Acids Res 2015; 44:917-25. [PMID: 26656490 PMCID: PMC4737153 DOI: 10.1093/nar/gkv1359] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. Previous studies showed that a 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE can reduce gene transcription by sequestering MAZ, a crucial transcription factor. Here we show that 32R-3n has to dimerize in order to fold into a G-quadruplex structure. Individual 5′- and 3′-end G-quadruplex units are formed and both feature a symmetric head-to-head topology with edge-type loops. The MAZ binding sequence is located within the 3′-end unit. Nuclear magnetic resonance data complemented by CD and UV spectra show that nucleotides of the MAZ binding G-rich motif are dynamic and could be available for sequence or structure based recognition. Both stable G-quadruplex structures could protect 5′- and 3′-ends of 32R-3n and enhance its anti-cancer activity. Single stranded genomic KRAS NHE including nucleotides flanking the 32R-3n sequence could favor a different monomeric fold, which remains unknown.
Collapse
Affiliation(s)
- Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
70
|
Morgan RK, Batra H, Gaerig VC, Hockings J, Brooks TA. Identification and characterization of a new G-quadruplex forming region within the kRAS promoter as a transcriptional regulator. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:235-45. [PMID: 26597160 DOI: 10.1016/j.bbagrm.2015.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
kRAS is one of the most prevalent oncogenic aberrations. It is either upregulated or mutationally activated in a multitude of cancers, including pancreatic, lung, and colon cancers. While a significant effort has been made to develop drugs that target kRAS, their clinical activity has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel mechanism and molecular target to downregulate kRAS expression--a previously undescribed G-quadruplex (G4) secondary structure within the proximal promoter acting as a transcriptional silencer. There are three distinct guanine-rich regions within the core kRAS promoter, including a previously examined region (G4near). Of these regions, the most distal region does not form an inducible and stable structure, whereas the two more proximal regions (termed near and mid) do form strong G4s. G4near is predominantly a tri-stacked structure with a discontinuous guanine run incorporated; G4mid consists of seven distinct runs of continuous guanines and forms numerous competing isoforms, including a stable three-tetrad stacked mixed parallel and antiparallel loop structures with longer loops of up to 10 nucleotides. Comprehensive analysis of the regulation of transcription by higher order structures has revealed that the guanine-rich region in the middle of the core promoter, termed G4mid, is a stronger repressor of promoter activity than G4near. Using the extensive guanine-rich region of the kRAS core promoter, and particularly the G4mid structure, as the primary target, future drug discovery programs will have potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic, ovarian, lung, and colon cancers.
Collapse
Affiliation(s)
- Rhianna K Morgan
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Harshul Batra
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Vanessa C Gaerig
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721, USA
| | - Jennifer Hockings
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Tracy A Brooks
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA.
| |
Collapse
|
71
|
Brito H, Martins AC, Lavrado J, Mendes E, Francisco AP, Santos SA, Ohnmacht SA, Kim NS, Rodrigues CMP, Moreira R, Neidle S, Borralho PM, Paulo A. Targeting KRAS Oncogene in Colon Cancer Cells with 7-Carboxylate Indolo[3,2-b]quinoline Tri-Alkylamine Derivatives. PLoS One 2015; 10:e0126891. [PMID: 26024321 PMCID: PMC4449006 DOI: 10.1371/journal.pone.0126891] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A guanine-rich strand within the promoter of the KRAS gene can fold into an intra-molecular G-quadruplex structure (G4), which has an important role in the regulation of KRAS transcription. We have previously identified indolo[3,2-b]quinolines with a 7-carboxylate group and three alkylamine side chains (IQ3A) as effective G4 stabilizers and promising selective anticancer leads. Herein we investigated the anticancer mechanism of action of these compounds, which we hypothesized due to stabilization of the G4 sequence in the KRAS promoter and subsequent down-regulation of gene expression. METHODOLOGY/PRINCIPAL FINDINGS IQ3A compounds showed greater stabilization of G4 compared to duplex DNA structures and reduced KRAS promoter activity in a dual luciferase reporter assay. Moreover, IQ3A compounds showed high anti-proliferative activity in HCT116 and SW620 colon cancer cells (IC50 < 2.69 μM), without eliciting cell death in non-malignant HEK293T human embryonic kidney, and human colon fibroblasts CCD18co. IQ3A compounds significantly reduced KRAS mRNA and protein steady-state levels at IC50 concentrations, and increased p53 protein steady-state levels and cell death by apoptosis in HCT116 cells (mut KRAS, wt p53). Furthermore, KRAS silencing in HCT116 p53 wild-type (p53(+/+)) and null (p53(-/-)) isogenic cell lines induced a higher level of cell death, and a higher IQ3A-induced cell death in HCT116 p53(+/+) compared to HCT116 p53(-/-). CONCLUSIONS Herein we provide evidence that G4 ligands such as IQ3A compounds can target G4 motifs present in KRAS promoter, down-regulate the expression of the mutant KRAS gene through inhibition of transcription and translation, and induce cell death by apoptosis in colon cancer cell lines. Thus, targeting KRAS at the genomic level with G4 ligands may be a new anticancer therapy strategy for colon cancer.
Collapse
Affiliation(s)
- Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Cláudia Martins
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Paula Francisco
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Sofia A. Santos
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Stephan A. Ohnmacht
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Cecília M. P. Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Pedro M. Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
| |
Collapse
|
72
|
Lavrado J, Brito H, Borralho PM, Ohnmacht SA, Kim NS, Leitão C, Pisco S, Gunaratnam M, Rodrigues CMP, Moreira R, Neidle S, Paulo A. KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines. Sci Rep 2015; 5:9696. [PMID: 25853628 PMCID: PMC5382548 DOI: 10.1038/srep09696] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/05/2015] [Indexed: 01/29/2023] Open
Abstract
KRAS is one of the most frequently mutated oncogenes in human cancer, yet remaining undruggable. To explore a new therapeutic strategy, a library of 5-methyl-indolo[3,2-c]quinoline derivatives (IQc) with a range of alkyldiamine side chains was designed to target DNA and RNA G-quadruplexes (G4) in the promoter and 5′-UTR mRNA of the KRAS gene. Biophysical experiments showed that di-substituted IQc compounds are potent and selective KRAS G4 stabilizers. They preferentially inhibit the proliferation of KRAS mutant cancer cell lines (0.22 < IC50 < 4.80 μM), down-regulate KRAS promoter activity in a luciferase reporter assay, and reduce both KRAS mRNA and p21KRAS steady-state levels in mutant KRAS colon cancer cell lines. Additionally, IQcs induce cancer cell death by apoptosis, explained in part by their capacity to repress KRAS expression. Overall, the results suggest that targeting mutant KRAS at the gene level with G4 binding small molecules is a promising anticancer strategy.
Collapse
Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Pedro M Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephan A Ohnmacht
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Clara Leitão
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Sílvia Pisco
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mekala Gunaratnam
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Cecília M P Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| |
Collapse
|
73
|
Zhao L, Wang P, Liu Y, Ma J, Xue Y. miR-34c regulates the permeability of blood-tumor barrier via MAZ-mediated expression changes of ZO-1, occludin, and claudin-5. J Cell Physiol 2015; 230:716-31. [PMID: 25201524 DOI: 10.1002/jcp.24799] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 09/05/2014] [Indexed: 11/11/2022]
Abstract
The purposes of this study were to investigate the potential roles of miR-34c in regulating blood-tumor barrier (BTB) functions and its possible molecular mechanisms. The over-expression of miR-34c significantly impaired the integrity and increased the permeability of BTB, which were detected in an in vitro BTB model by transendothelial electric resistance and horseradish peroxidase flux assays, respectively. Meanwhile, real-time quantitative PCR (qRT-PCR), Western blot and immunofluorescence assays successively demonstrated downregulation of ZO-1, occludin, and claudin-5 and miR-34c silencing uncovered the opposite results. Dual-luciferase reporter assays results revealed myc-associated zinc-finger protein (MAZ) is a target gene of miR-34c. Besides, mRNA and protein expressions of MAZ were reversely regulated by miR-34c. The down-expression of MAZ significantly impaired the integrity and increased the permeability of BTB as well as downregulated the expressions of ZO-1, occludin, and claudin-5. And chromatin immunoprecipitation verified that MAZ interacted with "GGGCGGG," "CCCTCCC," and "GGGAGGG" DNA sequence of ZO-1, occludin, and claudin-5 promoter, respectively. The over-expression or silencing of either miR-34c or MAZ was performed simultaneously to further explore their functional relations, and results elucidated that miR-34c and MAZ displayed reverse regulatory effects on the integrity and permeability of BTB as well as the expressions of ZO-1, occludin, and claudin-5. In conclusion, our present study indicated that miR-34c regulated the permeability of BTB via MAZ-mediated expression changes of ZO-1, occludin, and claudin-5.
Collapse
Affiliation(s)
- Lini Zhao
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang, People's Republic of China
| | | | | | | | | |
Collapse
|
74
|
Yao Y, Ma J, Xue Y, Wang P, Li Z, Li Z, Hu Y, Shang X, Liu Y. MiR-449a exerts tumor-suppressive functions in human glioblastoma by targeting Myc-associated zinc-finger protein. Mol Oncol 2014; 9:640-56. [PMID: 25487955 DOI: 10.1016/j.molonc.2014.11.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/14/2014] [Accepted: 11/14/2014] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma (GBM) is one of the most common and aggressive primary brain tumors in adults. Deregulated expression of microRNAs (miRNAs) has been associated with GBM progression through alterations in either oncogenic or tumor suppressor targets. Here, we elucidated the function and the possible molecular mechanisms of miR-449a in human GBM cell lines and tumor specimens-derived glioblastoma stem cells (GSCs). Quantitative real-time PCR demonstrated that miR-449a was down-regulated in human GBM cell lines and GSCs. Functionally, miR-449a acted as a tumor suppressor by reducing cell proliferation, migration and invasion as well as inducing apoptosis in human GBM cell lines and GSCs. Myc-associated zinc-finger protein (MAZ) was identified as a direct target of miR-449a, mediating these tumor-suppressive effects, demonstrated by Western blot assay and luciferase assays. Moreover, over-expression of miR-449a inhibited the expression of Podoplanin (PDPN) by down-regulating MAZ which could positively control the promoter activities via binding to the promoter of PDPN, demonstrated by luciferase assays and chromatin immunoprecipitation assays. Further, the PI3K/AKT pathway was blocked when MAZ was down-regulated by miR-449a. This process was coincided with the up-regulation of apoptotic proteins and the down-regulation of anti-apoptotic proteins, MMP2 and MMP9. Furthermore, nude mice carrying over-expressed miR-449a combined with knockdown MAZ tumors produced the smallest tumors and the highest survival. These results elucidated a novel molecular mechanism of GBM progression, and may thus suggest a promising application for GBM treatment.
Collapse
Affiliation(s)
- Yilong Yao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110001, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110001, People's Republic of China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110001, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110001, People's Republic of China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110001, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110001, People's Republic of China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China
| | - Zhiqing Li
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang 110001, People's Republic of China; Institute of Pathology and Pathophysiology, China Medical University, Shenyang 110001, People's Republic of China
| | - Yi Hu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China
| | - Xiuli Shang
- Department of Neurology, The First Affiliated Hospital, China Medical University, Shenyang 110001, People's Republic of China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, People's Republic of China.
| |
Collapse
|
75
|
DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
Collapse
|
76
|
Cogoi S, Shchekotikhin AE, Xodo LE. HRAS is silenced by two neighboring G-quadruplexes and activated by MAZ, a zinc-finger transcription factor with DNA unfolding property. Nucleic Acids Res 2014; 42:8379-88. [PMID: 25013182 PMCID: PMC4117790 DOI: 10.1093/nar/gku574] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The HRAS promoter contains immediately upstream of the transcription start site two neighboring G-elements, each capable of folding into a G-quadruplex structure. We have previously found that these G-quadruplexes bind to the zinc-finger transcription factors MAZ and Sp1. In the present study we have examined the interaction between the HRAS promoter and MAZ, demonstrating for the first time that the protein unfolds the G-quadruplex structures. We also demonstrate that MAZ-GST, in the presence of the complementary strands, promotes a rapid transformation of the two HRAS quadruplexes into duplexes. By a mutational analysis of the HRAS G-elements, we dissected the MAZ-binding sites from the quadruplex-forming motifs, finding that the two neighboring G-quadruplexes bring about a dramatic repression of transcription, in a synergistic manner. We also discovered that the two G-quadruplexes are strong targets for small anticancer molecules. We found that a cell-penetrating anthratiophenedione (ATPD-1), which binds tightly to the G-quadruplexes (ΔT > 15°C), promotes the total extinction of HRAS transcription. In contrast, when one of the two G-quadruplexes was abrogated by point mutations, ATPD-1 repressed transcription by only 50%. Our study provides relevant information for the rationale design of targeted therapy drugs specific for the HRAS oncogene.
Collapse
Affiliation(s)
- Susanna Cogoi
- Department of Medical and Biological Sciences, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
| | - Andrey E Shchekotikhin
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, B. Pirogovskaya, 11, Moscow 119021, Russia Mendeleyev University of Chemical Technology, 9 Miusskaya Square, Moscow 125190, Russia
| | - Luigi E Xodo
- Department of Medical and Biological Sciences, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
| |
Collapse
|
77
|
Cree SL, Kennedy MA. Relevance of G-quadruplex structures to pharmacogenetics. Front Pharmacol 2014; 5:160. [PMID: 25071578 PMCID: PMC4085647 DOI: 10.3389/fphar.2014.00160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022] Open
Abstract
G-quadruplexes are non-canonical secondary structures formed within nucleic acids that are involved in modulating cellular processes such as replication, gene regulation, recombination and epigenetics. Within genes, there is mounting evidence of G-quadruplex involvement in transcriptional and post transcriptional regulation. We report the presence of potential G-quadruplex motifs within relevant sites of some important pharmacogenes and discuss the possible implications of this on the function and expression of these genes. Appreciating the location and potential functions of these motifs may be of value when considering the impacts of some pharmacogenetic variants. G-quadruplexes are also the focus of drug development efforts in oncology and we highlight the broader pharmacological implications of treatment strategies that may target G-quadruplexes.
Collapse
Affiliation(s)
- Simone L Cree
- Department of Pathology, Carney Centre for Pharmacogenomics, University of Otago Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology, Carney Centre for Pharmacogenomics, University of Otago Christchurch, New Zealand
| |
Collapse
|
78
|
Russo Krauss I, Parkinson GN, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F. A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex. ACTA ACUST UNITED AC 2014; 70:362-70. [PMID: 24531470 DOI: 10.1107/s1399004713028095] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/13/2013] [Indexed: 01/19/2023]
Abstract
Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2' and C4' atoms are linked through a methylene bridge and the sugar is blocked in a 3'-endo conformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5'-TGGGT-3' is presented refined at 1.7 Å resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3'-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3'-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.
Collapse
Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Gary Nigel Parkinson
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, England
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Carlo Andrea Mattia
- Department of Pharmacy, University of Salerno, Via Ponte Don Melillo, I-84084 Fisciano, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples `Federico II', Via D. Montesano 49, I-80131 Napoli, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples `Federico II', Via D. Montesano 49, I-80131 Napoli, Italy
| | - Lelio Mazzarella
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, Via Cinthia, I-80126 Napoli, Italy
| |
Collapse
|
79
|
Abstract
MicroRNAs (miRNAs) are important regulators of diverse biologic processes. In the hematopoietic system, miRNAs have been shown to regulate lineage fate decisions, mature immune effector cell function, apoptosis, and cell cycling, and a more limited number of miRNAs has been shown to regulate hematopoietic stem cell (HSC) self-renewal. Many of these miRNAs were initially identified as candidate regulators of HSC function by comparing miRNA expression in hematopoietic stem and progenitors cells (HSPCs) to their mature progeny. While the measurement of miRNA expression in rare cell populations such as HSCs poses practical challenges due to the low amount of RNA present, a number of techniques have been developed to measure miRNAs in small numbers of cells. Here, we describe our protocol for measuring miRNAs in purified mouse HSCs using a highly sensitive real-time quantitative PCR strategy that utilizes microfluidic array cards containing pre-spotted TaqMan probes that allows the detection of mature miRNAs in small reaction volumes. We also describe a simple data analysis method to evaluate miRNA expression profiling data using an open-source software package (HTqPCR) using mouse HSC miRNA profiling data generated in our lab.
Collapse
Affiliation(s)
- Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | |
Collapse
|