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Princiotto S, Karelou M, Ioannidi R, Beretta GL, Zaffaroni N, Artali R, Kostakis IK, Mazzini S, Dallavalle S. Exploring the Interaction of New Pyridoquinazoline Derivatives with G-Quadruplex in the c-MYC Promoter Region. Int J Mol Sci 2023; 24:14346. [PMID: 37762650 PMCID: PMC10531603 DOI: 10.3390/ijms241814346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Novel amino-substituted pyridoquinazolinone derivatives have been designed and synthesized as potential c-MYC G-quadruplex (G4) ligands, employing an efficient methodology. All the new compounds exhibited moderate to good antiproliferative activity against the human osteosarcoma U2OS cell line. NMR and docking experiments revealed that the recently synthesized compounds interact with the Pu22 G-quadruplex in the c-MYC promoter region, establishing a 2:1 complex, with each molecule positioned over the tetrads at the 3'- and 5'-ends.
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Affiliation(s)
- Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (S.P.); (S.D.)
| | - Maria Karelou
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece; (M.K.); (R.I.)
| | - Rachel Ioannidi
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece; (M.K.); (R.I.)
| | - Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, 20133 Milan, Italy; (G.L.B.); (N.Z.)
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Via Amadeo 42, 20133 Milan, Italy; (G.L.B.); (N.Z.)
| | | | - Ioannis K. Kostakis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece; (M.K.); (R.I.)
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (S.P.); (S.D.)
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (S.P.); (S.D.)
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Bahls B, Aljnadi IM, Emídio R, Mendes E, Paulo A. G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy. Biomedicines 2023; 11:biomedicines11030969. [PMID: 36979947 PMCID: PMC10046398 DOI: 10.3390/biomedicines11030969] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is a societal burden demanding innovative approaches. A major problem with the conventional chemotherapeutic agents is their strong toxicity and other side effects due to their poor selectivity. Uncontrolled proliferation of cancer cells is due to mutations, deletions, or amplifications in genes (oncogenes) encoding for proteins that regulate cell growth and division, such as transcription factors, for example, c-MYC. The direct targeting of the c-MYC protein has been attempted but so far unsuccessfully, as it lacks a definite binding site for the modulators. Meanwhile, another approach has been explored since the discovery that G-quadruplex secondary DNA structures formed in the guanine-rich sequences of the c-MYC promoter region can downregulate the transcription of this oncogene. Here, we will overview the major achievements made in the last decades towards the discovery of a new class of anticancer drugs targeting G-quadruplexes in the c-MYC promoter of cancer cells.
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Affiliation(s)
- Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita Emídio
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
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Mayuri S, Jha NS. Fluorescent copper conjugated curcumin cysteine nanoprobe for selective determination of Fe 3+ and G-quadruplex DNA. Mikrochim Acta 2022; 190:17. [PMID: 36481915 DOI: 10.1007/s00604-022-05594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022]
Abstract
The synthesis of fluorescent copper-curcumin-cysteine (Cu-CC) as a sensing platform is reported. The synthesized probe has been confirmed by UV-visible spectroscopy, FT-IR, XRD, SEM, and TEM characterization techniques, respectively. The mechanistic aspects of selective sensing of Fe3+ and detection of different G-quadruplex DNA have been illustrated based on the "turn-off-on" concept of a regeneratable fluorescence sensing probe at λex 450 nm. Interestingly, we have noticed a high selectivity to Fe3+ ion by the developed Cu-CC sensing probe in comparison with other metal ions. Furthermore, the restoration of fluorescence of the sensing probe in the presence of different DNA sequences is illustrating a cost-effective, convenient, and reliable detection methodology of DNA detection. It is highly sensitive for the determination of Pu27, promoter c-MYC quadruplex DNA in a wide linear range of 100-700 nM having a detection limit of 13.1 nM (RSD: 0.15%) and sensitivity of 37.2 cps/nM. Whereas, the Pu18 and H-telo telomeric DNA sequences are showing a narrow linear range, i.e., 10 nM-200 nM and 10 nM-180 nM, respectively. The real-world sample analysis performance of the regeneratable sensing probe for Pu27 DNA detection in fresh human blood serum samples is showing a satisfactory result.
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Affiliation(s)
- Sanyukta Mayuri
- Department of Chemistry, National Institute of Technology Patna, Ashok Rajpath, Patna, 800005, India
| | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology Patna, Ashok Rajpath, Patna, 800005, India.
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Sharma S, Mukherjee AK, Roy SS, Bagri S, Lier S, Verma M, Sengupta A, Kumar M, Nesse G, Pandey DP, Chowdhury S. Human telomerase is directly regulated by non-telomeric TRF2-G-quadruplex interaction. Cell Rep 2021; 35:109154. [PMID: 34010660 PMCID: PMC7611063 DOI: 10.1016/j.celrep.2021.109154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) remains suppressed in most normal somatic cells. Resulting erosion of telomeres leads eventually to replicative senescence. Reactivation of hTERT maintains telomeres and triggers progression of >90% of cancers. However, any direct causal link between telomeres and telomerase regulation remains unclear. Here, we show that the telomere-repeat-binding-factor 2 (TRF2) binds hTERT promoter G-quadruplexes and recruits the polycomb-repressor EZH2/PRC2 complex. This is causal for H3K27 trimethylation at the hTERT promoter and represses hTERT in cancer as well as normal cells. Two highly recurrent hTERT promoter mutations found in many cancers, including ∼83% glioblastoma multiforme, that are known to destabilize hTERT promoter G-quadruplexes, showed loss of TRF2 binding in patient-derived primary glioblastoma multiforme cells. Ligand-induced G-quadruplex stabilization restored TRF2 binding, H3K27-trimethylation, and hTERT re-suppression. These results uncover a mechanism of hTERT regulation through a telomeric factor, implicating telomere-telomerase molecular links important in neoplastic transformation, aging, and regenerative therapy.
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Affiliation(s)
- Shalu Sharma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Shuvra Shekhar Roy
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Silje Lier
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Meenakshi Verma
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Antara Sengupta
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manish Kumar
- Imaging Facility, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Gaute Nesse
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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Engin AB, Engin A. The Connection Between Cell Fate and Telomere. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1275:71-100. [PMID: 33539012 DOI: 10.1007/978-3-030-49844-3_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abolition of telomerase activity results in telomere shortening, a process that eventually destabilizes the ends of chromosomes, leading to genomic instability and cell growth arrest or death. Telomere shortening leads to the attainment of the "Hayflick limit", and the transition of cells to state of senescence. If senescence is bypassed, cells undergo crisis through loss of checkpoints. This process causes massive cell death concomitant with further telomere shortening and spontaneous telomere fusions. In functional telomere of mammalian cells, DNA contains double-stranded tandem repeats of TTAGGG. The Shelterin complex, which is composed of six different proteins, is required for the regulation of telomere length and stability in cells. Telomere protection by telomeric repeat binding protein 2 (TRF2) is dependent on DNA damage response (DDR) inhibition via formation of T-loop structures. Many protein kinases contribute to the DDR activated cell cycle checkpoint pathways, and prevent DNA replication until damaged DNA is repaired. Thereby, the connection between cell fate and telomere length-associated telomerase activity is regulated by multiple protein kinase activities. Contrarily, inactivation of DNA damage checkpoint protein kinases in senescent cells can restore cell-cycle progression into S phase. Therefore, telomere-initiated senescence is a DNA damage checkpoint response that is activated with a direct contribution from dysfunctional telomeres. In this review, in addition to the above mentioned, the choice of main repair pathways, which comprise non-homologous end joining and homologous recombination in telomere uncapping telomere dysfunctions, are discussed.
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Affiliation(s)
- Ayse Basak Engin
- Department of Toxicology, Faculty of Pharmacy, Gazi University, Ankara, Turkey.
| | - Atilla Engin
- Department of General Surgery, Faculty of Medicine, Gazi University, Ankara, Turkey
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Pavlova II, Tsvetkov VB, Isaakova EA, Severov VV, Khomyakova EA, Lacis IA, Lazarev VN, Lagarkova MA, Pozmogova GE, Varizhuk AM. Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures. Int J Biol Macromol 2020; 160:1144-1157. [PMID: 32454109 DOI: 10.1016/j.ijbiomac.2020.05.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Affinity for G-quadruplex (G4) structures may be a common feature of transcription-facilitating histone chaperons (HCs). This assumption is based on previous unmatched studies of HCs FACT, nucleolin (NCL), BRD3, and ATRX. We verified this assumption and considered its implications for the therapeutic applications of synthetic (exogenous) G4s and the biological significance of genomic G4s. First, we questioned whether exogenous G4s that recognize cell-surface NCL and could trap other HCs in the nucleus are usable as anticancer agents. We performed in vitro binding assays and selected leading multi-targeted G4s. They exhibited minor effects on cell viability. The presumed NCL-regulated intracellular transport of G4s was inefficient or insufficient for tumor-specific G4 delivery. Next, to clarify whether G4s in the human genome could recruit HCs, we compared available HC ChIP-seq data with G4-seq/G4-ChIP-seq data. Several G4s, including the well-known c-Myc quadruplex structure, were found to be colocalized with HC occupancy sites in cancer cell lines. As evidenced by our molecular modeling data, c-Myc G4 might interfere with the HC function of BRD3 but is unlikely to prevent the BRD3-driven assembly of the chromatin remodeling complex. The c-Myc case illustrates the intricate role of genomic G4s in chromatin remodeling, nucleosome remodeling, and transcription.
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Affiliation(s)
- Iulia I Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow 119146, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow 119991, Russia
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vyacheslav V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ekaterina A Khomyakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ivan A Lacis
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia; Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991, Russia.
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Abstract
Circular dichroism and stopped-flow UV spectroscopies were used to investigate the thermodynamic stability and the folding pathway of d[TGAG3TG3TAG3TG3TA2] at 25 °C in solutions containing 25 mM KCl. Under these conditions the oligonucleotide adopts a thermally stable, all-parallel G-quadruplex topography containing three stacked quartets. K+-induced folding shows three resolved relaxation times, each with distinctive spectral changes. Folding is complete within 200 s. These data indicate a folding pathway that involves at least two populated intermediates, one of which seems to be an antiparallel structure that rearranges to the final all-parallel conformation. Molecular dynamics reveals a stereochemically plausible folding pathway that does not involve complete unfolding of the intermediate. The rate of unfolding was determined using complementary DNA to trap transiently unfolded states to form a stable duplex. As assessed by 1D-1H NMR and fluorescence spectroscopy, unfolding is extremely slow with only one observable rate-limiting relaxation time.
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Muench D, Rezzoug F, Thomas SD, Xiao J, Islam A, Miller DM, Sedoris KC. Quadruplex-forming oligonucleotide targeted to the VEGF promoter inhibits growth of non-small cell lung cancer cells. PLoS One 2019; 14:e0211046. [PMID: 30682194 PMCID: PMC6347295 DOI: 10.1371/journal.pone.0211046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Vascular endothelial growth factor (VEGF) is commonly overexpressed in a variety of tumor types including lung cancer. As a key regulator of angiogenesis, it promotes tumor survival, growth, and metastasis through the activation of the downstream protein kinase B (AKT) and extracellular signal-regulated kinase (ERK 1/2) activation. The VEGF promoter contains a 36 bp guanine-rich sequence (VEGFq) which is capable of forming quadruplex (four-stranded) DNA. This sequence has been implicated in the down-regulation of both basal and inducible VEGF expression and represents an ideal target for inhibition of VEGF expression. RESULTS Our experiments demonstrate sequence-specific interaction between a G-rich quadruplex-forming oligonucleotide encoding a portion of the VEGFq sequence and its double stranded target sequence, suggesting that this G-rich oligonucleotide binds specifically to its complementary C-rich sequence in the genomic VEGF promoter by strand invasion. We show that treatment of A549 non-small lung cancer cells (NSCLC) with this oligonucleotide results in decreased VEGF expression and growth inhibition. The VEGFq oligonucleotide inhibits proliferation and invasion by decreasing VEGF mRNA/protein expression and subsequent ERK 1/2 and AKT activation. Furthermore, the VEGFq oligonucleotide is abundantly taken into cells, localized in the cytoplasm/nucleus, inherently stable in serum and intracellularly, and has no effect on non-transformed cells. Suppression of VEGF expression induces cytoplasmic accumulation of autophagic vacuoles and increased expression of LC3B, suggesting that VEGFq may induce autophagic cell death. CONCLUSION Our data strongly suggest that the G-rich VEGFq oligonucleotide binds specifically to the C-rich strand of the genomic VEGF promoter, via strand invasion, stabilizing the quadruplex structure formed by the genomic G-rich sequence, resulting in transcriptional inhibition. Strand invading oligonucleotides represent a new approach to specifically inhibit VEGF expression that avoids many of the problems which have plagued the therapeutic use of oligonucleotides. This is a novel approach to specific inhibition of gene expression.
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Affiliation(s)
- David Muench
- Department of Immunobiology, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Francine Rezzoug
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Shelia D. Thomas
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Jingjing Xiao
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Ashraful Islam
- Faculty of Medicine, University of Tabuk, Tabuk, Saudi Arabia
| | - Donald M. Miller
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail:
| | - Kara C. Sedoris
- Department of Physiology, University of Louisville, Louisville, Kentucky, United States of America
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Zhu J, Fleming AM, Burrows CJ. The RAD17 Promoter Sequence Contains a Potential Tail-Dependent G-Quadruplex That Downregulates Gene Expression upon Oxidative Modification. ACS Chem Biol 2018; 13:2577-2584. [PMID: 30063821 DOI: 10.1021/acschembio.8b00522] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our laboratory has recently proposed that the oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in G-rich promoter regions of DNA repair genes can serve as a regulatory mechanism of gene transcription. These regions also have the potential to fold into G-quadruplexes (G4). The human RAD17 promoter sequence has such a region in the template strand of the gene. In this work, the potential G-quadruplex sequence (PQS) of the RAD17 gene promoter was analyzed in different sequence contexts. With two extra nucleotides of the native sequence on either side of the G4, the structure was found to fold into a hybrid-like G4, similar to the hybrid-1 fold that the human telomere sequence can adopt. With only one nucleotide on either side of the PQS, the topology of the structure was observed to be mixed, and without extra nucleotides on the ends, the sequence adopted a parallel fold. Next, the sequence was studied with synthetic incorporation of the oxidative modification OG into specific sites and installed into the promoter of plasmids with a luciferase gene. These plasmids were transfected into a human cell line to observe the effect of the G4s on transcription. The RAD17 PQS was found to decrease luciferase expression with the presence of OG that is consistent with RAD17 expression under oxidative stress. This serves as an example of how oxidative modification could affect transcription in the context of a G4.
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Affiliation(s)
- Judy Zhu
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, United States
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Huang C, Li R, Zhang Y, Gong J. Amarogentin Induces Apoptosis of Liver Cancer Cells via Upregulation of p53 and Downregulation of Human Telomerase Reverse Transcriptase in Mice. Technol Cancer Res Treat 2017; 16:546-558. [PMID: 27402632 PMCID: PMC5665146 DOI: 10.1177/1533034616657976] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 04/27/2016] [Accepted: 06/06/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Amarogentin has been reported to have a preventive effect on liver cancer via inducing cancer cell apoptosis. We attempted to elucidate the roles of p53-associated apoptosis pathways in the chemopreventive mechanism of amarogentin. The findings of this study will facilitate the development of a novel supplementary strategy for the treatment of liver cancer. MATERIALS AND METHODS The purity of amarogentin was assessed by high-performance liquid chromatography. The inhibitory ratios of the liver cell lines were determined using a Cell Counting Kit-8 following treatment with a gradient concentration of amarogentin. Cell apoptosis was detected by flow cytometry using annexin V-fluorescein isothiocyanate/propidium iodide kits. The gene and protein expression of p53-associated molecules, such as Akt, human telomerase reverse transcriptase, RelA, and p38, was detected by real-time quantitative polymerase chain reaction, Western blotting, and immunohistochemical staining in liver cancer cells and mouse tumor tissues after treatment with amarogentin. RESULTS The inhibitory effect of amarogentin on cell proliferation was more obvious in liver cancer cells, and amarogentin was more likely to induce the apoptosis of liver cancer cells than that of normal liver cells. The gene and protein expression levels of Akt, RelA, and human telomerase reverse transcriptase were markedly higher in the control group than in the preventive group and treatment groups. Only the expression of human telomerase reverse transcriptase was downregulated, accompanied by the upregulation of p53. CONCLUSION The results of our study suggest that amarogentin promotes apoptosis of liver cancer cells by the upregulation of p53 and downregulation of human telomerase reverse transcriptase and prevents the malignant transformation of these cells.
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Affiliation(s)
- Chun Huang
- Chongqing Key Laboratory of Hepatobiliary Surgery, Department of Hepatobiliary Surgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Division of Basic Medical Science, Chongqing Three Gorges Medical College, Chongqing, Wanzhou, People’s Republic of China
| | - Runqin Li
- Division of Basic Medical Science, Chongqing Three Gorges Medical College, Chongqing, Wanzhou, People’s Republic of China
- Department of Histology and Embryology, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yinglin Zhang
- Department of Hepatobiliary Surgery, The Third Hospital of Mianyang, Mianyang, Sichuan, People’s Republic of China
| | - Jianping Gong
- Chongqing Key Laboratory of Hepatobiliary Surgery, Department of Hepatobiliary Surgery, Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
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Gomez DLM, Armando RG, Cerrudo CS, Ghiringhelli PD, Gomez DE. Telomerase as a Cancer Target. Development of New Molecules. Curr Top Med Chem 2017; 16:2432-40. [PMID: 26873194 PMCID: PMC4997958 DOI: 10.2174/1568026616666160212122425] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/15/2015] [Accepted: 10/25/2015] [Indexed: 12/26/2022]
Abstract
Telomeres are the terminal part of the chromosome containing a long repetitive and non-codifying sequence that has as function protecting the chromosomes. In normal cells, telomeres lost part of such repetitive sequence in each mitosis, until telomeres reach a critical point, triggering at that time senescence and cell death. However, in most of tumor cells in each cell division a part of the telomere is lost, however the appearance of an enzyme called telomerase synthetize the segment that just has been lost, therefore conferring to tumor cells the immortality hallmark. Telomerase is significantly overexpressed in 80–95% of all malignant tumors, being present at low levels in few normal cells, mostly stem cells. Due to these characteristics, telomerase has become an attractive target for new and more effective anticancer agents. The capability of inhibiting telomerase in tumor cells should lead to telomere shortening, senescence and apoptosis. In this work, we analyze the different strategies for telomerase inhibition, either in development, preclinical or clinical stages taking into account their strong points and their caveats. We covered strategies such as nucleosides analogs, oligonucleotides, small molecule inhibitors, G-quadruplex stabilizers, immunotherapy, gene therapy, molecules that affect the telomere/telomerase associated proteins, agents from microbial sources, among others, providing a balanced evaluation of the status of the inhibitors of this powerful target together with an analysis of the challenges ahead.
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Affiliation(s)
| | | | | | | | - D E Gomez
- Laboratory of Molecular Oncology, Department of Science and Technology. Quilmes National University, Bernal, Buenos Aires, Argentina. R. Saenz Peña 352, (1876) Buenos Aires, Argentina.
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12
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Zhao Z, Lin F, Ye H, Huang R, Xu X. Effects of modified-guanosine on the stability of G-triplex. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.10.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Hao T, Gaerig VC, Brooks TA. Nucleic acid clamp-mediated recognition and stabilization of the physiologically relevant MYC promoter G-quadruplex. Nucleic Acids Res 2016; 44:11013-11023. [PMID: 27789698 PMCID: PMC5159522 DOI: 10.1093/nar/gkw1006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 10/18/2016] [Indexed: 01/24/2023] Open
Abstract
The MYC proto-oncogene is upregulated, often at the transcriptional level, in ∼80% of all cancers. MYC's promoter is governed by a higher order G-quadruplex (G4) structure in the NHE III1 region. Under a variety of conditions, multiple isoforms have been described to form from the first four continuous guanine runs (G41–4) predominating under the physiologically relevant supercoiled conditions. In the current study, short oligonucleotides complementing the 5′- and 3′-regions flanking the G4 have been connected by an abasic linker to form G4 clamps, varying both linker length and G4 isoform being targeted. Clamp A with an 18 Å linker was found to have marked affinity for its target isomer (G41–4) over the other major structures (G42–5 and G41–5, recognized by clamps B and C, respectively), and to be able to shift equilibrating DNA to foster greater G4 formation. In addition, clamp A, but not B or C, is able to modulate MYC promoter activity with a significant and dose-dependent effect on transcription driven by the Del4 plasmid. This linked clamp-mediated approach to G4 recognition represents a novel therapeutic mechanism with specificity for an individual promoter structure, amenable to a large array of promoters.
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Affiliation(s)
- Taisen Hao
- BioMolecular Sciences, University of Mississippi, University, MS 38677, USA
| | - Vanessa C Gaerig
- Pharmacy, Charleston Area Medical Center Memorial Hospital, Charleston, WV 25304, USA
| | - Tracy A Brooks
- BioMolecular Sciences, University of Mississippi, University, MS 38677, USA
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14
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Byrd AK, Zybailov BL, Maddukuri L, Gao J, Marecki JC, Jaiswal M, Bell MR, Griffin WC, Reed MR, Chib S, Mackintosh SG, MacNicol AM, Baldini G, Eoff RL, Raney KD. Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress. J Biol Chem 2016; 291:18041-57. [PMID: 27369081 DOI: 10.1074/jbc.m116.718478] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 12/13/2022] Open
Abstract
Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA). In response to oxidative stress, we demonstrate that sequences capable of forming G4DNA appear at increasing levels in the cytoplasm and participate in assembly of stress granules. Identified proteins that bind to endogenous G4DNA in the cytoplasm are known to modulate mRNA translation and participate in stress granule formation. Consistent with these findings, stress granule formation is known to regulate mRNA translation during oxidative stress. We propose a signaling pathway whereby cells can rapidly respond to DNA damage caused by oxidative stress. Guanine-rich sequences that are excised from damaged genomic DNA are proposed to enter the cytoplasm where they can regulate translation through stress granule formation. This newly proposed role for G4DNA provides an additional molecular explanation for why such sequences are prevalent in the human genome.
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Affiliation(s)
- Alicia K Byrd
- From the Departments of Biochemistry and Molecular Biology and
| | - Boris L Zybailov
- From the Departments of Biochemistry and Molecular Biology and the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Leena Maddukuri
- From the Departments of Biochemistry and Molecular Biology and
| | - Jun Gao
- From the Departments of Biochemistry and Molecular Biology and
| | - John C Marecki
- From the Departments of Biochemistry and Molecular Biology and
| | - Mihir Jaiswal
- the University of Arkansas at Little Rock/University of Arkansas for Medical Sciences (UALR/UAMS) Joint Graduate Program in Bioinformatics, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Matthew R Bell
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Megan R Reed
- From the Departments of Biochemistry and Molecular Biology and
| | - Shubeena Chib
- From the Departments of Biochemistry and Molecular Biology and
| | - Samuel G Mackintosh
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Angus M MacNicol
- the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and Neurobiology and Developmental Sciences and
| | - Giulia Baldini
- From the Departments of Biochemistry and Molecular Biology and
| | - Robert L Eoff
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
| | - Kevin D Raney
- From the Departments of Biochemistry and Molecular Biology and the Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 and
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15
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Mechanism studies on anti-HepG2 cell proliferation of phenanthroline derivatives as G-quadruplex DNA stabilizers. Bioorg Med Chem Lett 2015; 25:3798-803. [DOI: 10.1016/j.bmcl.2015.07.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/06/2015] [Accepted: 07/25/2015] [Indexed: 12/13/2022]
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16
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Scuotto M, Rivieccio E, Varone A, Corda D, Bucci M, Vellecco V, Cirino G, Virgilio A, Esposito V, Galeone A, Borbone N, Varra M, Mayol L. Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Res 2015; 43:7702-16. [PMID: 26250112 PMCID: PMC4652776 DOI: 10.1093/nar/gkv789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.
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Affiliation(s)
- Maria Scuotto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Elisa Rivieccio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
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17
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Chen BJ, Wu YL, Tanaka Y, Zhang W. Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics. Int J Biol Sci 2014; 10:1084-96. [PMID: 25332683 PMCID: PMC4202025 DOI: 10.7150/ijbs.10190] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
The nuclear transcription factor c-Myc is a member of the Myc gene family with multiple functions and located on band q24.1 of chromosome 8. The c-Myc gene is activated by chromosomal translocation, rearrangement, and amplification. Its encoded protein transduces intracellular signals to the nucleus, resulting in the regulation of cell proliferation, differentiation, and apoptosis, and has the ability to transform cells and bind chromosomal DNA. c-Myc also plays a critical role in malignant transformation. The abnormal over-expression of c-Myc is frequently observed in some tumors, including carcinomas of the breast, colon, and cervix, as well as small-cell lung cancer, osteosarcomas, glioblastomas, and myeloid leukemias, therefore making it a possible target for anticancer therapy. In this minireview, we summarize unique characteristics of c-Myc and therapeutic strategies against cancer using small molecules targeting the oncogene, and discuss the prospects in the development of agents targeting c-Myc, in particular G-quadruplexes formed in c-Myc promoter and c-Myc/Max dimerization. Such information will be of importance for the research and development of c-Myc-targeted drugs.
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Affiliation(s)
- Bing-Jia Chen
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yan-Ling Wu
- 2. Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, 630 Xincheng Road, Hangzhou, 310051, China. ; 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yoshimasa Tanaka
- 3. Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Wen Zhang
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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18
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Müller S, Rodriguez R. G-quadruplex interacting small molecules and drugs: from bench toward bedside. Expert Rev Clin Pharmacol 2014; 7:663-79. [DOI: 10.1586/17512433.2014.945909] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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