1
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Dai Y, Teng X, Zhang Q, Hou H, Li J. Advances and challenges in identifying and characterizing G-quadruplex-protein interactions. Trends Biochem Sci 2023; 48:894-909. [PMID: 37422364 DOI: 10.1016/j.tibs.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
G-quadruplexes (G4s) are peculiar nucleic acid secondary structures formed by DNA or RNA and are considered as fundamental features of the genome. Many proteins can specifically bind to G4 structures. There is increasing evidence that G4-protein interactions involve in the regulation of important cellular processes, such as DNA replication, transcription, RNA splicing, and translation. Additionally, G4-protein interactions have been demonstrated to be potential targets for disease treatment. In order to unravel the detailed regulatory mechanisms of G4-binding proteins (G4BPs), biochemical methods for detecting G4-protein interactions with high specificity and sensitivity are highly demanded. Here, we review recent advances in screening and validation of new G4BPs and highlight both their features and limitations.
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Affiliation(s)
- Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; New Cornerstone Science Laboratory, Shenzhen 518054, China
| | - Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; New Cornerstone Science Laboratory, Shenzhen 518054, China
| | - Qiushuang Zhang
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; New Cornerstone Science Laboratory, Shenzhen 518054, China
| | - Hongwei Hou
- Beijing Life Science Academy, Beijing 102209, China.
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China; New Cornerstone Science Laboratory, Shenzhen 518054, China; Beijing Life Science Academy, Beijing 102209, China; Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, Anhui, China.
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2
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Iwasaki Y, Ookuro Y, Iida K, Nagasawa K, Yoshida W. Destabilization of DNA and RNA G-quadruplex structures formed by GGA repeat due to N 6-methyladenine modification. Biochem Biophys Res Commun 2022; 597:134-139. [PMID: 35144176 DOI: 10.1016/j.bbrc.2022.01.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenine (m6A) is the most abundant RNA modification in eukaryotic RNA. Further, m6A has been identified in the genomic DNA of both eukaryotes and prokaryotes. The G-quadruplex (G4) structure is a non-canonical nucleic acid structure formed by the stacking of G:G:G:G tetrads. In this study, we evaluated the effect of m6A modifications on G4 structures formed by GGA repeat oligonucleotides, d(GGA)8, d(GGA)4, and r(GGA)4. The d(GGA)8 forms an intramolecular tetrad:heptad:heptad:tetrad G4 structure, while d(GGA)4 forms a dimerized intermolecular tetrad:heptad:heptad:tetrad G4 structure. r(GGA)4 forms a dimerized intermolecular tetrad:hexad:hexad:tetrad G4 structure. Circular dichroism melting analysis demonstrated that (1) m6A modifications destabilized the G4 structure formed by d(GGA)8, (2) m6A modification at A3 disrupted the G4 structure formed by d(GGA)4, and (3) m6A modification at A3 destabilized the G4 structure formed by r(GGA)4. m6A modifications may be involved in controlling G4 structure formation to regulate biological functions.
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Affiliation(s)
- Yuka Iwasaki
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Yurino Ookuro
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
| | - Keisuke Iida
- Department of Chemistry, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan; School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan.
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3
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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4
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Linke R, Limmer M, Juranek SA, Heine A, Paeschke K. The Relevance of G-Quadruplexes for DNA Repair. Int J Mol Sci 2021; 22:12599. [PMID: 34830478 PMCID: PMC8620898 DOI: 10.3390/ijms222212599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023] Open
Abstract
DNA molecules can adopt a variety of alternative structures. Among these structures are G-quadruplex DNA structures (G4s), which support cellular function by affecting transcription, translation, and telomere maintenance. These structures can also induce genome instability by stalling replication, increasing DNA damage, and recombination events. G-quadruplex-driven genome instability is connected to tumorigenesis and other genetic disorders. In recent years, the connection between genome stability, DNA repair and G4 formation was further underlined by the identification of multiple DNA repair proteins and ligands which bind and stabilize said G4 structures to block specific DNA repair pathways. The relevance of G4s for different DNA repair pathways is complex and depends on the repair pathway itself. G4 structures can induce DNA damage and block efficient DNA repair, but they can also support the activity and function of certain repair pathways. In this review, we highlight the roles and consequences of G4 DNA structures for DNA repair initiation, processing, and the efficiency of various DNA repair pathways.
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Affiliation(s)
- Rebecca Linke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaela Limmer
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Stefan A. Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
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5
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Gao Z, Williams P, Li L, Wang Y. A Quantitative Proteomic Approach for the Identification of DNA Guanine Quadruplex-Binding Proteins. J Proteome Res 2021; 20:4919-4924. [PMID: 34570971 DOI: 10.1021/acs.jproteome.1c00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA sequences of high guanine (G) content have the potential to form G quadruplex (G4) structures. A more complete understanding about the biological functions of G4 DNA requires the investigation about how these structures are recognized by proteins. Here, we conducted exhaustive quantitative proteomic experiments to profile the interaction proteomes of G4 structures by employing different sequences of G4 DNA derived from the human telomere and the promoters of c-MYC and c-KIT genes. Our results led to the identification of a number of candidate G4-interacting proteins, many of which were discovered here for the first time. These included three proteins that can bind to all three DNA G4 structures and 78 other proteins that can bind selectively to one or two of the three DNA G4 structure(s). We also validated that GRSF1 can bind directly and selectively toward G4 structure derived from the c-MYC promoter. Our quantitative proteomic screening also led to the identification of a number of candidate "antireader" proteins of G4 DNA. Together, we uncovered a number of cellular proteins that exhibit general and selective recognitions of G4 folding patterns, which underscore the complexity of G4 DNA in biology and the importance of understanding fully the G4-interaction proteome.
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Affiliation(s)
- Zi Gao
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Preston Williams
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
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6
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Morrissey KL, DeWitt D, Shah N, Fall W, Shah H, McGown LB. Comparison of protein capture from a human cancer cell line by genomic G-quadruplex DNA sequences toward aptamer discovery. Anal Bioanal Chem 2021; 413:3775-3788. [PMID: 33884462 DOI: 10.1007/s00216-021-03328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022]
Abstract
A genome-inspired route to aptamer discovery that expands the sequence space beyond that available in traditional, combinatorial selection approaches is investigated for discovery of DNA-protein interactions in cancer. These interactions could then serve as the basis for new DNA aptamers to cancer-related proteins. The genome-inspired approach uses specific DNA sequences from the human genome to capture proteins from biological protein pools. The use of naturally occurring DNA sequences takes advantage of biological evolution of DNA sequences that bind to specific proteins to perform biological functions. Linking aptamer discovery to nature increa`ses the chances of uncovering protein-DNA affinity binding interactions that have biological significance as well as analytical utility. Here, the focus is on genomic, G-rich sequences that can form G-quadruplex (G4) structures. These structures are underrepresented in combinatorial libraries used for conventional aptamer selection. Additionally, G4-forming sequences are prone to inefficient PCR amplification, further biasing aptamer selection away from these structures. Nature provides a large diversity of G4-forming sequences throughout the human genome. They are prevalent in gene promoter regions, especially in oncogene promoters, and are therefore promising candidates for aptamers to regulatory proteins in cancer. The present work investigates protein capture from nuclear and cytoplasmic extracts of the breast cancer cell line MDA-MB-468 by G4-forming sequences from the CMYC, RB, and VEGF gene promoters. The studies included the effects of modifications of the VEGF sequence on the selectivity of protein capture, from which we identified promising aptamer candidates, subject to further refinement, to the proteins nucleolin and RPL19, both of which play important regulatory functions related to cancer.
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Affiliation(s)
- Kathleen L Morrissey
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Dylan DeWitt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Nikhil Shah
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - William Fall
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Hari Shah
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Linda B McGown
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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7
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Cui X, Chen H, Zhang Q, Xu M, Yuan G, Zhou J. Exploration of the Structure and Recognition of a G-quadruplex in the her2 Proto-oncogene Promoter and Its Transcriptional Regulation. Sci Rep 2019; 9:3966. [PMID: 30850693 PMCID: PMC6408435 DOI: 10.1038/s41598-019-39941-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/23/2019] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes in oncogene promoters provide putative targets for transcriptional regulation. The structure of a putative G-quadruplex sequence (S1: GGAGAAGGAGGAGGTGGAGGAGGAGGG) in potassium solution in the her2 promoter has been resolved mainly through nuclear magnetic resonance (NMR) spectroscopy. By application of various NMR spectra, we proved the formation of a four-layer G-quadruplex composing of two G-tetrads and two G/A-mixed planes with a four-residues loop (A3-G4-A5-A6). Further evidence from a luciferase reporter assay, Q-RT-PCR and Western blotting indicates that S1 G-quadruplex formation can repress her2 promoter activity, and a selected G-quadruplex ligand cβ can enhance the repression by down regulating her2 transcription and expression. These findings provide a G-quadruplex target and perspective implications in her2 transcriptional regulation.
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Affiliation(s)
- Xiaojie Cui
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Han Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Department of Cardiology, Peking University Third Hospital, Beijing, 100191, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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8
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Abstract
Chromosomal rearrangements, including translocations, are early and essential events in the formation of many tumors. Previous studies that defined the genetic requirements for rearrangement formation have identified differences between murine and human cells, most notably in the role of classic and alternative nonhomologous end-joining (NHEJ) factors. We reported that poly(ADP)ribose polymerase 3 (PARP3) promotes chromosomal rearrangements induced by endonucleases in multiple human cell types. We show here that in contrast to classic (c-NHEJ) factors, Parp3 also promotes rearrangements in murine cells, including translocations in murine embryonic stem cells (mESCs), class-switch recombination in primary B cells, and inversions in tail fibroblasts that generate Eml4-Alk fusions. In mESCs, Parp3-deficient cells had shorter deletion lengths at translocation junctions. This was corroborated using next-generation sequencing of Eml4-Alk junctions in tail fibroblasts and is consistent with a role for Parp3 in promoting the processing of DNA double-strand breaks. We confirmed a previous report that Parp1 also promotes rearrangement formation. In contrast with Parp3, rearrangement junctions in the absence of Parp1 had longer deletion lengths, suggesting that Parp1 may suppress double-strand break processing. Together, these data indicate that Parp3 and Parp1 promote rearrangements with distinct phenotypes.
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9
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Albanese CM, Suttapitugsakul S, Perati S, McGown LB. A genome-inspired, reverse selection approach to aptamer discovery. Talanta 2017; 177:150-156. [PMID: 29108569 DOI: 10.1016/j.talanta.2017.08.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 11/29/2022]
Abstract
Limitations of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and related methods that depend upon combinatorial oligonucleotide libraries have hindered progress in this area. Our laboratory has introduced a new approach to aptamer discovery that uses oligonucleotides with sequences drawn from the human genome to capture proteins from biological samples. Specifically, we have focused on capture of proteins in nuclear extracts from human cell lines using G-quadruplex (G4) forming genomic sequences. Previous studies identified capture of several proteins both in vitro and in live cells by the Pu28-mer sequence from the ERBB2 promoter region. Here we provide a more comprehensive study of protein capture from BT474 and MCF7 human breast cancer cells using G4-forming sequences from the CMYC, RB, VEGF and ERBB2 human oncogene promoter regions. Mass spectrometric analysis and Western blot analysis of protein capture at oligonucleotide-modified surfaces revealed capture of nucleolin by all three of the oligonucleotides in BT474 and MCF7 cells, and also of ribosomal protein L19 (RPL19) in BT474 cells. Chromatin immunoprecipitation (ChIP) analysis confirmed the interaction of nucleolin with all three promoter sequences in MCF7 cells and with RB in BT474 cells. ChIP also revealed interactions of RPL19 with CMYC in BT474 cells and of both RPL19 and ribosomal protein L14 (RPL14) with ERBB2 in BT474 cells. These results offer the basis for development of new aptamers based on the G4 sequences from the CMYC, RB, VEGF, and ERBB2 promoters toward proteins including nucleolin, RPL19 and RPL14. These interactions also may have biological and therapeutic significance.
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Affiliation(s)
- Christina M Albanese
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Suttipong Suttapitugsakul
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Shruthi Perati
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Linda B McGown
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
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10
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Garg R, Aggarwal J, Thakkar B. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants. Sci Rep 2016; 6:28211. [PMID: 27324275 PMCID: PMC4914980 DOI: 10.1038/srep28211] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/18/2016] [Indexed: 11/22/2022] Open
Abstract
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Aggarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bijal Thakkar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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11
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Gollamudi J, Parvani JG, Schiemann WP, Vinayak S. Neoadjuvant therapy for early-stage breast cancer: the clinical utility of pertuzumab. Cancer Manag Res 2016; 8:21-31. [PMID: 26937204 PMCID: PMC4762586 DOI: 10.2147/cmar.s55279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Approximately 20% of breast cancer patients harbor tumors that overexpress human epidermal growth factor receptor 2 (HER2; also known as ErbB2), a receptor tyrosine kinase that belongs to the epidermal growth factor receptor family of receptor tyrosine kinases. HER2 amplification and hyperactivation drive the growth and survival of breast cancers through the aberrant activation of proto-oncogenic signaling systems, particularly the Ras/MAP kinase and PI3K/AKT pathways. Although HER2-positive (HER2(+)) breast cancer was originally considered to be a highly aggressive form of the disease, the clinical landscape of HER2(+) breast cancers has literally been transformed by the approval of anti-HER2 agents for adjuvant and neoadjuvant settings. Indeed, pertuzumab is a novel monoclonal antibody that functions as an anti-HER2 agent by targeting the extracellular dimerization domain of the HER2 receptor; it is also the first drug to receive an accelerated approval by the US Food and Drug Administration for use in neoadjuvant settings in early-stage HER2(+) breast cancer. Here, we review the molecular and cellular factors that contribute to the pathophysiology of HER2 in breast cancer, as well as summarize the landmark preclinical and clinical findings underlying the approval and use of pertuzumab in the neoadjuvant setting. Finally, the molecular mechanisms operant in mediating resistance to anti-HER2 agents, and perhaps to pertuzumab as well, will be discussed, as will the anticipated clinical impact and future directions of pertuzumab in breast cancer patients.
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Affiliation(s)
- Jahnavi Gollamudi
- Department of Internal Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jenny G Parvani
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - William P Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Shaveta Vinayak
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Hematology and Oncology, University Hospitals Case Medical Center, Cleveland, OH, USA
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12
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Pagano B, Margarucci L, Zizza P, Amato J, Iaccarino N, Cassiano C, Salvati E, Novellino E, Biroccio A, Casapullo A, Randazzo A. Identification of novel interactors of human telomeric G-quadruplex DNA. Chem Commun (Camb) 2015; 51:2964-7. [DOI: 10.1039/c4cc07231f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Starting from a chemoproteomic-driven approach, novel human telomeric G-quadruplex binding proteins were identified that directly bind the DNA structure in vitro and colocalize with such structures in cells.
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Affiliation(s)
- Bruno Pagano
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | | | - Pasquale Zizza
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | - Jussara Amato
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Nunzia Iaccarino
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Chiara Cassiano
- Department of Pharmacy
- University of Salerno
- 84084 Fisciano
- Italy
| | - Erica Salvati
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | - Ettore Novellino
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- 00158 Rome
- Italy
| | | | - Antonio Randazzo
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Napoli
- Italy
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13
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Guo ZM, Li W, Zhao XH. Purine-rich element binding protein alpha promotes invasion and migration of esophageal squamous cell carcinoma KYSE 510 cells by inducing epithelial-mesenchymal transition. Shijie Huaren Xiaohua Zazhi 2014; 22:5579-5586. [DOI: 10.11569/wcjd.v22.i36.5579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the role of purine-rich element binding protein alpha (PURα) in the invasion and migration of esophageal squamous cell carcinoma (ESCC) KYSE 510 cells and the underlying mechanisms.
METHODS: An ESCC cell line overexpressing PURα (KYSE 510-PURα) was established, and the expression levels of epithelial-mesenchymal transition associated proteins were determined by comparing with control cells transfected with an empty vector of pCMV6 (KYSE 510-pCMV6). The expression of E-cadherin and vimentin was analyzed by Western blot and immunofluorescent staining. The capabilities of invasion and migration of cancer cells were assessed via transwell and wound healing assays.
RESULTS: PURα was overexpressed in KYSE 510 cells transfected with the pCMV6- PURα vector. The expression of E-cadherin was reduced, and that of Vimentin, N-cadherin and Snail was increased in KYSE 510-PURα cells. Most strikingly, the cell morphology was changed as fibroblasts and the abilities of migration and invasion were altered.
CONCLUSION: Our data suggest that regulation of PURα expression in ESCC cells may induce esophageal epithelial-mesenchymal transition.
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Dittrich A, Gautrey H, Browell D, Tyson-Capper A. The HER2 Signaling Network in Breast Cancer--Like a Spider in its Web. J Mammary Gland Biol Neoplasia 2014; 19:253-70. [PMID: 25544707 DOI: 10.1007/s10911-014-9329-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/14/2014] [Indexed: 12/21/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) is a major player in the survival and proliferation of tumour cells and is overexpressed in up to 30 % of breast cancer cases. A considerable amount of work has been undertaken to unravel the activity and function of HER2 to try and develop effective therapies that impede its action in HER2 positive breast tumours. Research has focused on exploring the HER2 activated phosphoinositide-3-kinase (PI3K)/AKT and rat sarcoma/mitogen-activated protein kinase (RAS/MAPK) pathways for therapies. Despite the advances, cases of drug resistance and recurrence of disease still remain a challenge to overcome. An important aspect for drug resistance is the complexity of the HER2 signaling network. This includes the crosstalk between HER2 and hormone receptors; its function as a transcription factor; the regulation of HER2 by protein-tyrosine phosphatases and a complex network of positive and negative feedback-loops. This review summarises the current knowledge of many different HER2 interactions to illustrate the complexity of the HER2 network from the transcription of HER2 to the effect of its downstream targets. Exploring the novel avenues of the HER2 signaling could yield a better understanding of treatment resistance and give rise to developing new and more effective therapies.
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Affiliation(s)
- A Dittrich
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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15
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Cassidy LM, Burcar BT, Stevens W, Moriarty EM, McGown LB. Guanine-centric self-assembly of nucleotides in water: an important consideration in prebiotic chemistry. ASTROBIOLOGY 2014; 14:876-886. [PMID: 25285982 PMCID: PMC4201266 DOI: 10.1089/ast.2014.1155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 09/03/2014] [Indexed: 06/03/2023]
Abstract
Investigations of plausible prebiotic chemistry on early Earth must consider not only chemical reactions to form more complex products such as proto-biopolymers but also reversible, molecular self-assembly that would influence the availability, organization, and sequestration of reactant molecules. The self-assembly of guanosine compounds into higher-order structures and lyotropic liquid crystalline "gel" phases through formation of hydrogen-bonded guanine tetrads (G-tetrads) is one such consideration that is particularly relevant to an RNA-world scenario. G-tetrad-based gelation has been well studied for individual guanosine compounds and was recently observed in mixtures of guanosine with 5'-guanosine monophosphate (GMP) as well. The present work investigates the self-assembly of GMP in the presence of the other RNA nucleotides. Effects of the total concentration and relative proportion of the nucleotides in the mixtures, the form (disodium salt vs. free acid) of the nucleotides, temperature, pH, and salt concentration were determined by visual observations and circular dichroism (CD) spectroscopy. The results show that formation of cholesteric G-tetrad phases is influenced by interactions with other nucleotides, likely through association (e.g., intercalation) of the nucleotides with the G-tetrad structures. These interactions affect the structure and stability of the G-tetrad gel phase, as well as the formation of alternate self-assembled GMP structures such as a continuous, hydrogen-bonded GMP helix or dimers and aggregates of GMP. These interactions and multiple equilibria are influenced by the presence of cations, especially in the presence of K(+). This work could have important implications for the emergence of an RNA or proto-RNA world, which would require mixtures of nucleotides at sufficiently high, local concentrations for abiotic polymerization to occur.
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Affiliation(s)
- Lauren M Cassidy
- New York Center for Astrobiology and Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
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Musumeci D, Amato J, Randazzo A, Novellino E, Giancola C, Montesarchio D, Pagano B. G-Quadruplex on Oligo Affinity Support (G4-OAS): An Easy Affinity Chromatography-Based Assay for the Screening of G-Quadruplex Ligands. Anal Chem 2014; 86:4126-30. [DOI: 10.1021/ac500444m] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Domenica Musumeci
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Napoli, Italy
| | - Jussara Amato
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, 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
| | - Concetta Giancola
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
| | - Daniela Montesarchio
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Napoli, Italy
| | - Bruno Pagano
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
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