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Wu C, Nilsson K, Zheng Y, Ekenstierna C, Sugiyama N, Forslund O, Kajitani N, Yu H, Wennerberg J, Ekblad L, Schwartz S. Short half-life of HPV16 E6 and E7 mRNAs sensitizes HPV16-positive tonsillar cancer cell line HN26 to DNA-damaging drugs. Int J Cancer 2019; 144:297-310. [PMID: 30303514 PMCID: PMC6587446 DOI: 10.1002/ijc.31918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022]
Abstract
Here we show that treatment of the HPV16-positive tonsillar cancer cell line HN26 with DNA alkylating cancer drug melphalan-induced p53 and activated apoptosis. Melphalan reduced the levels of RNA polymerase II and cellular transcription factor Sp1 that were associated with HPV16 DNA. The resulting inhibition of transcription caused a rapid loss of the HPV16 early mRNAs encoding E6 and E7 as a result of their inherent instability. As a consequence of HPV16 E6 and E7 down-regulation, the DNA damage inflicted on the cells by melphalan caused induction of p53 and activation of apoptosis in the HN26 cells. The BARD1-negative phenotype of the HN26 cells may have contributed to the failure to repair DNA damage caused by melphalan, as well as to the efficient apoptosis induction. Finally, nude mice carrying the HPV16 positive tonsillar cancer cells responded better to melphalan than to cisplatin, the chemotherapeutic drug of choice for tonsillar cancer. We concluded that the short half-life of the HPV16 E6 and E7 mRNAs renders HPV16-driven tonsillar cancer cells particularly sensitive to DNA damaging agents such as melphalan since melphalan both inhibits transcription and causes DNA damage.
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Affiliation(s)
- Chengjun Wu
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Kersti Nilsson
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Yunji Zheng
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Camilla Ekenstierna
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Skane University Hospital, Lund, Sweden
| | - Natsuki Sugiyama
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Skane University Hospital, Lund, Sweden
| | - Ola Forslund
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Naoko Kajitani
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Haoran Yu
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Johan Wennerberg
- Department of Clinical Sciences Lund, Oto-rhino-laryngology, Head and Neck Surgery, Lund University, Skane University Hospital, Lund, Sweden
| | - Lars Ekblad
- Department of Clinical Sciences Lund, Oncology and Pathology, Lund University, Skane University Hospital, Lund, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, Lund, Sweden
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Onel B, Wu G, Sun D, Lin C, Yang D. Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein Complexes. Methods Mol Biol 2019; 2035:201-222. [PMID: 31444751 DOI: 10.1007/978-1-4939-9666-7_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA G-quadruplexes are globular nucleic acid secondary structures which occur throughout the human genome under physiological conditions. There is accumulating evidence supporting G-quadruplex involvement in a number of important aspects of genome functions, including transcription, replication, and genomic stability, and that protein and enzyme recognition of G-quadruplexes may represent a key event to regulate physiological or pathological pathways. Two important techniques to study G-quadruplexes and their protein interactions are the electrophoretic mobility shift assay (EMSA) and dimethyl sulfate (DMS) footprinting assay. EMSA, one of the most sensitive and robust methods for studying the DNA-protein interactions, can be used to determine the binding parameters and relative affinities of a protein for the G-quadruplex. DMS footprinting is a powerful assay for the initial characterization of G-quadruplexes, which can be used to deduce the guanine bases involved in the formation of G-tetrads under physiological salt conditions. DMS footprinting can also reveal important information in G-quadruplex-protein complexes on protein contacts and regional changes in DNA G-quadruplex upon protein binding. In this paper, we will provide a detailed protocol for the EMSA and DMS footprinting assays for characterization of G-quadruplexes and G-quadruplex-protein complexes. Expected outcomes and references to extensions of the method will be further discussed.
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Affiliation(s)
- Buket Onel
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Guanhui Wu
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Daekyu Sun
- University of Arizona, College of Pharmacy, Tucson, AZ, USA.,BIO5 Institute, Tucson, AZ, USA.,Arizona Cancer Center, Tucson, AZ, USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA. .,Purdue Center for Cancer Research, West Lafayette, IN, USA. .,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.
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Zhang S, Lei X, Huo P, Liu Q, Guan X, Jiang J, Shi D, Lu F. The effects of IAM38 blocking or CD4 blocking on the binding of exogenous DNA in rabbit sperm. Mol Biol Rep 2018; 46:251-259. [PMID: 30415444 DOI: 10.1007/s11033-018-4466-3] [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: 09/04/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022]
Abstract
The binding of exogenous DNA to sperm is a key process for sperm-mediated gene transfer; however, the underlying molecular mechanisms have yet to be elucidated. In the present study, we aimed to identify the DNA binding proteins (DBPs) in rabbit sperm and to gain further understanding of the molecular mechanism of sperm and exogenous DNA interaction. Native polyacrylamide gel electrophoresis was used for separating free sperm proteins and complexes of DNA fragment/sperm proteins. A distinct band was found after Coomassie blue staining, and seven potential proteins were identified by mass spectrometry analysis. An analysis of the physical/chemical properties of the seven proteins revealed that the sperm inner acrosomal membrane protein IAM38 (IAM38) matched the features of the DBPs. Western blotting analysis showed that the IAM38 and CD4 were present in the sperm but not in the seminal plasma. Blocking of the IAM38 impaired the DNA-binding capacity of the sperm. Blocking the CD4 decreased the DNA-uptake capacity of the sperm but did not influence the DNA-binding capacity of the sperm. Moreover, the EGFP-positive embryos and EGFP-positive blastocysts were also decreased after IAM38 blocking or CD4 blocking in comparison with the control group. In conclusion, our results imply that foreign DNA first binds to the transmembrane IAM38 of the sperm plasma membrane and then forms the complex of DNA/IAM38/CD4 with CD4 to complete the transportation of exogenous DNA into the nucleus of sperm.
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Affiliation(s)
- Shun Zhang
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.,Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiaocan Lei
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Peng Huo
- School of Public Health of Guilin Medical University, Guilin, China
| | - Qingyou Liu
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Xiaomei Guan
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Jianrong Jiang
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Deshun Shi
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Fenghua Lu
- Guangxi High Education Key Laboratory for Animal Reproduction and Biotechnology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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Warner KD, Sjekloća L, Song W, Filonov GS, Jaffrey SR, Ferré-D’Amaré AR. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol 2017; 13:1195-1201. [PMID: 28945234 PMCID: PMC5663454 DOI: 10.1038/nchembio.2475] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
Abstract
Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures.
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Affiliation(s)
- Katherine Deigan Warner
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Grigory S. Filonov
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell
University, New York, New York, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood
Institute, Bethesda, Maryland, USA
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Shan W, Cui Y, Liu M, Wu L, Xiang Y, Guo Q, Zhang Z, Huang Y. Systematic evaluation of the toxicity and biodistribution of virus mimicking mucus-penetrating DLPC-NPs as oral drug delivery system. Int J Pharm 2017; 530:89-98. [DOI: 10.1016/j.ijpharm.2017.07.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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6
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Song C, Zhang S, Huang H. Choosing a suitable method for the identification of replication origins in microbial genomes. Front Microbiol 2015; 6:1049. [PMID: 26483774 PMCID: PMC4588119 DOI: 10.3389/fmicb.2015.01049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.
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Affiliation(s)
- Chengcheng Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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