1
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Singh SK, Kumar R, Mathur M, Kamboj H, Kaushik JK, Mohanty AK, Kumar S. Exploring aptamers for targeted enrichment of X sperm in bovine: unraveling selective potential. Anim Biotechnol 2024; 35:2323592. [PMID: 38770771 DOI: 10.1080/10495398.2024.2323592] [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] [Indexed: 05/22/2024]
Abstract
Nucleic acid aptamers have been used in the past for the development of diagnostic methods against a number of targets such as bacteria, pesticides, cancer cells etc. In the present study, six rounds of Cell-SELEX were performed on a ssDNA aptamer library against X-enriched sperm cells from Sahiwal breed cattle. Sequencing was used to examine the aptamer sequences that shown affinity for sperm carrying the X chromosome in order to find any possible X-sperm-specific sequences. Out of 35 identified sequences, 14 were selected based on bioinformatics analysis like G-Score and Mfold structures. Further validation of their specificity was done via fluorescence microscopy. The interaction of biotinylated-aptamer with sperm was also determined by visualizing the binding of streptavidin coated magnetic beads on the head region of the sperm under bright field microscopy. Finally, a real-time experiment was designed for the validation of X-sperm enrichment by synthesized aptamer sequences. Among the studied sequences, aptamer 29a exhibited a higher affinity for X sperm compared to Y sperm in a mixed population of sperm cells. By using aptamer sequence 29a, we obtained an enrichment of 70% for X chromosome bearing sperm cells.
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Affiliation(s)
| | | | - Manya Mathur
- National Dairy Research Institute (ICAR), Karnal, Haryana, India
| | - Himanshu Kamboj
- Amity Institute of Biotechnology, Amity University, Noida, India
| | | | - Ashok Kumar Mohanty
- National Dairy Research Institute (ICAR), Karnal, Haryana, India
- Central Institute for Research on Cattle, Meerut, Uttar Pradesh, India
| | - Sudarshan Kumar
- National Dairy Research Institute (ICAR), Karnal, Haryana, India
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2
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Herrera A, Zhou J, Song MS, Rossi JJ. Evolution of Cell-Type-Specific RNA Aptamers via Live Cell-Based SELEX. Methods Mol Biol 2023; 2666:317-346. [PMID: 37166674 DOI: 10.1007/978-1-0716-3191-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Live cell-based SELEX (Systematic Evolution of Ligand EXponential enrichment) is a promising approach for identifying aptamers that can selectively bind to a cell-surface receptor or recognize a particular target cell population. In particular, it offers a facile selection strategy for some special cell-surface proteins that are originally glycosylated or heavily posttranslationally modified and are unavailable in their native/active conformation after in vitro expression and purification. In this chapter, we describe a generalized procedure for evolution of cell type-specific RNA aptamers targeting a cell membrane bound target by combining the live cell-based SELEX strategy with high-throughput sequencing (HTS) and bioinformatics analysis.
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Affiliation(s)
- Alberto Herrera
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | | | - Min-Sun Song
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - John J Rossi
- Center for RNA Biology and Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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3
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Narayan C, Veeramani S, Thiel WH. Optimization of RNA Aptamer SELEX Methods: Improved Aptamer Transcript 3'-End Homogeneity, PAGE Purification Yield, and Target-Bound Aptamer RNA Recovery. Nucleic Acid Ther 2022; 32:74-80. [PMID: 34757856 PMCID: PMC8817694 DOI: 10.1089/nat.2021.0060] [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] [Indexed: 02/03/2023] Open
Abstract
Since its inception in the early 1990s, SELEX remains the gold standard for discovering RNA aptamers specific for proteins and small molecules. The SELEX process has undergone countless modifications and now encompasses a breadth of innovative selection schemes to pare an aptamer library toward target-specific aptamers. Common to all these RNA aptamer SELEX processes are the steps for the preparation of DNA template and in vitro transcription of aptamer RNA. These steps have remained mostly unchanged over the past three decades and would benefit from optimization. We focused on three key areas: improving the homogeneity of in vitro transcribed aptamer RNA, increasing the efficiency of in vitro transcribed aptamer RNA purification by PAGE, and improving the quality of target-bound aptamer RNA recovered during SELEX. Together, these optimizations contribute toward a more efficient SELEX process and are applicable to both protein-based and cell-based RNA aptamer selections.
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Affiliation(s)
- Chandan Narayan
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA
| | - Suresh Veeramani
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Department of Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: Suresh Veeramani, DVM, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William H. Thiel
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: William H. Thiel, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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4
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Xia F, He A, Zhao H, Sun Y, Duan Q, Abbas SJ, Liu J, Xiao Z, Tan W. Molecular Engineering of Aptamer Self-Assemblies Increases in Vivo Stability and Targeted Recognition. ACS NANO 2022; 16:169-179. [PMID: 34935348 DOI: 10.1021/acsnano.1c05265] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Functionally modified aptamer conjugates are promising tools for targeted imaging or treatment of various diseases. However, broad applications of aptamer molecules are limited by their in vivo instability. To overcome this challenge, current strategies mostly rely on covalent chemical modification of aptamers, a complicated process that requires case-by-case sequence design, multiple-step synthesis, and purification. Herein, we report a covalent modification-free strategy to enhance the in vivo stability of aptamers. This strategy simply utilizes one-step molecular engineering of aptamers with gold nanoclusters (GNCs) to form GNCs@aptamer self-assemblies. Using Sgc8 as a representative aptamer, the resulting GNCs@Sgc8 assemblies enhance cancer-cell-specific binding and sequential internalization by a receptor-mediated endocytosis pathway. Importantly, the GNCs@aptamer self-assemblies resist nuclease degradation for as long as 48 h, compared to the degradation of aptamer alone at 3 h. In parallel, the tumor-targeted recognition and retention of GNCs@aptamer self-assemblies are dramatically enhanced, indicated by a 9-fold signal increase inside the tumor compared to the aptamer alone. This strategy is to avoid complicated chemical modification of aptamers and can be extended to all aptamers. Our work provides a simple, effective, and universal strategy for enhancing the in vivo stability of any aptamer or its conjugates, thus expanding their imaging and therapeutic applications.
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Affiliation(s)
- Fangfang Xia
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Axin He
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haitao Zhao
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiao Duan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sk Jahir Abbas
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
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5
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Zhang W, Teske N, Samadi M, Sarem M, Shastri VP. Unraveling the role of β1 integrin isoforms in cRGD-mediated uptake of nanoparticles bearing hydrophilized alkyne moieties in epithelial and endothelial cells. Acta Biomater 2020; 116:344-355. [PMID: 32871280 DOI: 10.1016/j.actbio.2020.08.038] [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: 05/22/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023]
Abstract
The uptake and trafficking of NPs is impacted by several attributes such as size, shape, surface charge and importantly by surface ligands that can interact with the cell plasma membrane. We envision that NPs which can be readily modified in aqueous environments will be key to engineering patient-specific nanotherapeutics. Towards such systems that can be functionalized "on demand" in aqueous environments, an α-ω epoxy ester monomer that bears an alkyne group at the end of an oligoethylene glycol moiety was designed and synthesized. Copolymerization of this monomer with ε-caprolactone yielded polymers that present hydrophilized alkyne groups along the backbone. This enabled the direct modification of the surface of NPs, as suspensions in aqueous phase, with cell interaction peptides such cyclic-arginine-glycine-aspartic acid (cRGD) using the "click reaction". Uptake of cRGD modified NPs (cRGD-NPs) in human endothelial and tumor epithelial cells revealed that cRGD surprisingly diminished uptake in both tumor epithelial and microvascular endothelial cells by 40-50 percent in comparison to unmodified particles. Probing the mechanism of uptake revealed that the expression pattern of two isoforms of β1 integrin impacted the uptake of cRGD-NPs differently. While the expression of high molecular weight 140 kDa form of the β1 integrin enhanced NP uptake, the expression of low molecular 120 kDa form had an inhibitory effect. Furthermore, although, the expression of β3 integrin was enhanced in endothelial cells and breast cancer epithelial cells, no correlation between β3 integrin and NP uptake was observed. Additionally, in presence of clathrin and caveolae pathway inhibitors the uptake of cRGD-NPS was in general diminished with a 25-75% decrease in presence of Filipin, a caveolae inhibitor; suggesting a role for lipid rafts in the β1 integrin-mediated uptake of cRGD-NP NPs. In sum, the polymer system described can be readily adapted to engineer other targeting peptide-based nanotherapeutics, especially for the delivery across difficult penetrate biological barriers such as the blood brain barrier. The main findings of this study have significant implication for the development of integrin targeted nanotherapeutics for anti-tumor therapy.
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Affiliation(s)
- Weihai Zhang
- Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Nele Teske
- Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Mariam Samadi
- Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Melika Sarem
- Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - V Prasad Shastri
- Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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6
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Xuan W, Peng Y, Deng Z, Peng T, Kuai H, Li Y, He J, Jin C, Liu Y, Wang R, Tan W. A basic insight into aptamer-drug conjugates (ApDCs). Biomaterials 2018; 182:216-226. [PMID: 30138784 DOI: 10.1016/j.biomaterials.2018.08.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022]
Abstract
Aptamers are often compared with antibodies since both types of molecules function as targeting ligands for specific cancer cell recognition. However, aptamers offer several advantages, including small size, facile chemical modification, high chemical stability, low immunogenicity, rapid tissue penetration, and engineering simplicity. Despite these advantages, several crucial factors have delayed their clinical translation, such as concerns over inherent physicochemical stability and safety. Meanwhile, steps have been taken to make aptamer-drug conjugates, or ApDCs, a clinically practical tool. In this review, we highlight the development of ApDCs and discuss how researchers are solving some problems associated with their clinical application for targeted therapy.
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Affiliation(s)
- Wenjing Xuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yongbo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhengyu Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tianhuan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yingying Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jiaxuan He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ruowen Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, College of Chemistry and Chemical Engineering, Shanghai 200240, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China; Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, College of Chemistry and Chemical Engineering, Shanghai 200240, China; Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States.
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7
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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8
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Longmate W, DiPersio CM. Beyond adhesion: emerging roles for integrins in control of the tumor microenvironment. F1000Res 2017; 6:1612. [PMID: 29026524 PMCID: PMC5583736 DOI: 10.12688/f1000research.11877.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
While integrins were originally discovered as cell adhesion receptors, recent studies have reinforced the concept that integrins have central roles in cancer that extend far beyond controlling cell adhesion and migration. Indeed, as transmembrane cell surface receptors that occupy a critical position at the interface of cellular and extracellular interactions and are capable of both "inside-out" and "outside-in" signaling, integrins are uniquely poised to regulate the cell's ability to promote, sense, and react to changes in the tumor microenvironment. Moreover, integrins are present on all cell types in the tumor microenvironment, and they have important roles in regulating intercellular communication. Decades of promising pre-clinical studies have implicated certain integrins as attractive therapeutic targets in the cancer clinic. Nevertheless, results of the few clinical trials that target integrins in cancer have thus far been disappointing. Importantly, these clinical failures likely reflect the emerging complexity of individual and combinatorial integrin function within both tumor cells and other cell types of the tumor microenvironment, together with a need to explore integrin-targeting agents not just as monotherapies but also as adjuvants to more conventional radiotherapies or chemotherapies. In this review, we will examine recent advances toward understanding how integrins regulate cancer progression, including their roles in intercellular communication and modulation of the tumor microenvironment. Additionally, we will discuss factors that underlie the limited efficacy of current efforts to target integrins in the cancer clinic as well as potential strategies to overcome these challenges.
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Affiliation(s)
- Whitney Longmate
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - C Michael DiPersio
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA.,Department of Surgery, Albany Medical College, Albany , New York, USA
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9
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Volk DE, Lokesh GLR. Development of Phosphorothioate DNA and DNA Thioaptamers. Biomedicines 2017; 5:E41. [PMID: 28703779 PMCID: PMC5618299 DOI: 10.3390/biomedicines5030041] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers are short RNA- or DNA-based affinity reagents typically selected from combinatorial libraries to bind to a specific target such as a protein, a small molecule, whole cells or even animals. Aptamers have utility in the development of diagnostic, imaging and therapeutic applications due to their size, physico-chemical nature and ease of synthesis and modification to suit the application. A variety of oligonucleotide modifications have been used to enhance the stability of aptamers from nuclease degradation in vivo. The non-bridging oxygen atoms of the phosphodiester backbones of RNA and DNA aptamers can be substituted with one or two sulfur atoms, resulting in thioaptamers with phosphorothioate or phosphorodithioate linkages, respectively. Such thioaptamers are known to have increased binding affinity towards their target, as well as enhanced resistance to nuclease degradation. In this review, we discuss the development of phosphorothioate chemistry and thioaptamers, with a brief review of selection methods.
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Affiliation(s)
- David E Volk
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Ganesh L R Lokesh
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
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10
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Nanotechnology and nanocarrier-based approaches on treatment of degenerative diseases. INTERNATIONAL NANO LETTERS 2017. [DOI: 10.1007/s40089-017-0208-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Yan M, Zhu C, Huang Y, Yan J, Chen A. Ultrasensitive detection of lead(II) using a turn-on probe based on the use of an aptamer and a water-soluble fluorescent perylene probe. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2292-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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13
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Zhen S, Takahashi Y, Narita S, Yang YC, Li X. Targeted delivery of CRISPR/Cas9 to prostate cancer by modified gRNA using a flexible aptamer-cationic liposome. Oncotarget 2017; 8:9375-9387. [PMID: 28030843 PMCID: PMC5354738 DOI: 10.18632/oncotarget.14072] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022] Open
Abstract
The potent ability of CRISPR/Cas9 system to inhibit the expression of targeted gene is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of CRISPR/Cas9 into specific cell populations is still the principal challenge in the clinical development of CRISPR/Cas9 therapeutics. In this study, a flexible aptamer-liposome-CRISPR/Cas9 chimera was designed to combine efficient delivery and increased flexibility. Our chimera incorporated an RNA aptamer that specifically binds prostate cancer cells expressing the prostate-specific membrane antigen as a ligand. Cationic liposomes were linked to aptamers by the post-insertion method and were used to deliver therapeutic CRISPR/Cas9 that target the survival gene, polo-like kinase 1, in tumor cells. We demonstrate that the aptamer-liposome-CRISPR/Cas9 chimeras had a significant cell-type binding specificity and a remarkable gene silencing effect in vitro. Furthermore, silencing promoted a conspicuous regression of prostate cancer in vivo. Importantly, the approach described here provides a universal means of cell type-specific CRISPR/Cas9 delivery, which is a critical goal for the widespread therapeutic applicability of CRISPR/Cas9 or other nucleic acid drugs.
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MESH Headings
- Animals
- Apoptosis
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Cations
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Clustered Regularly Interspaced Short Palindromic Repeats
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Gene Targeting/methods
- Gene Transfer Techniques
- Genetic Therapy/methods
- Humans
- Kallikreins/metabolism
- Liposomes
- Male
- Mice, Nude
- Prostate-Specific Antigen/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/therapy
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Xenograft Model Antitumor Assays
- Polo-Like Kinase 1
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Affiliation(s)
- Shuai Zhen
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, P.R. China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, P.R. China
| | - Yoichiro Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shunichi Narita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yi-Chen Yang
- Tsinghua University, School of Life Sciences, Beijing, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, P.R. China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, P.R. China
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14
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Abstract
Live cell-based SELEX (Systematic Evolution of Ligand EXponential enrichment) is a promising approach for identifying aptamers that can selectively bind to a cell-surface antigen or a particular target cell population. In particular, it offers a facile selection strategy for some special cell-surface proteins that are original glycosylated or heavily post-translationally modified, and are unavailable in their native/active conformation after in vitro expression and purification. In this chapter, we describe evolution of cell-type-specific RNA aptamers targeting the human CCR5 by combining the live cell-based SELEX strategy with high-throughput sequencing (HTS) and bioinformatics analysis.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Rd, Duarte, CA, 91010, USA
| | - John J Rossi
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Rd, Duarte, CA, 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Rd, Duarte, CA, 91010, USA.
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15
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Binzel DW, Khisamutdinov E, Vieweger M, Ortega J, Li J, Guo P. Mechanism of three-component collision to produce ultrastable pRNA three-way junction of Phi29 DNA-packaging motor by kinetic assessment. RNA (NEW YORK, N.Y.) 2016; 22:1710-1718. [PMID: 27672132 PMCID: PMC5066623 DOI: 10.1261/rna.057646.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/09/2016] [Indexed: 05/27/2023]
Abstract
RNA nanotechnology is rapidly emerging. Due to advantageous pharmacokinetics and favorable in vivo biodistribution, RNA nanoparticles have shown promise in targeted delivery of therapeutics. RNA nanotechnology applies bottom-up assembly, thus elucidation of the mechanism of interaction between multiple components is of fundamental importance. The tendency of diminishing concern about RNA instability has accelerated by the finding of the novel thermostable three-way junction (3WJ) motif of the phi29 DNA-packaging motor. The kinetics of these three components, each averaging 18 nucleotides (nt), was investigated to elucidate the mechanism for producing the stable 3WJ. The three fragments coassembled into the 3WJ with extraordinary speed and affinity via a two-step reaction mechanism, 3WJb + 3WJc ↔ 3WJbc + 3WJa ↔ 3WJabc The first step of reaction between 3WJb and 3WJc is highly dynamic since these two fragments only contain 8 nt for complementation. In the second step, the 3WJa, which contains 17 nt complementary to the 3WJbc complex, locks the unstable 3WJbc complex into a highly stable 3WJ. The resulting pRNA-3WJ is more stable than any of the dimer species as shown in the much more rapid association rates and slowest dissociation rate constant. The second step occurs at a very high association rate that is difficult to quantify, resulting in a rapid formation of a stable 3WJ. Elucidation of the mechanism of three-component collision in producing the ultrastable 3WJ proves a promising platform for bottom-up assembly of RNA nanoparticles as a new class of anion polymers for material science, electronic elements, or therapeutic reagents.
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Affiliation(s)
- Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Emil Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Mario Vieweger
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Janice Ortega
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA
| | - Jingyuan Li
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China, 1000049
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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16
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Takahashi M, Sakota E, Nakamura Y. The efficient cell-SELEX strategy, Icell-SELEX, using isogenic cell lines for selection and counter-selection to generate RNA aptamers to cell surface proteins. Biochimie 2016; 131:77-84. [PMID: 27693080 DOI: 10.1016/j.biochi.2016.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/26/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Abstract
Aptamers are short single-stranded nucleic acid molecules that are selected in vitro from a large random sequence library based on their high and specific affinity to a target molecule by a process known as SELEX. Cell-SELEX that employs whole living cells overexpressing the defined cell surface proteins (for selection) and appropriate mock cells (for counter-selection) has been widely used as a valid and feasible method for generating aptamers against specific cell surface proteins. However, the endogenous expression of target proteins in mock cells or the heterogeneity of surface proteins between selection and counter-selection cells often impeded the isolation of proper aptamers against target proteins. To solve this problem, we developed "Isogenic cell-SELEX" (Icell SELEX in short) method, in which isogenic cell lines were manipulated for counter-selection by microRNA-mediated silencing and for selection by overexpression of target proteins. As a model experiment, we targeted integrin alpha V (ITGAV), which is a major transmembrane receptor expressed in almost all the cells, and established ITGAV-overexpressed and -downregulated HEK293 cells for selection and counter-selection, respectively. By taking advantage of a hundred-fold difference in the expression level of ITGAV between these two isogenic cell lines, we easily isolated several anti-ITGAV aptamers, whose binding to the cell-surface ITGAV was confirmed by flow cytometry with the dissociation constant of 300-400 nM range. We assume that Icell-SELEX could be applicable to a wide range of cell-surface proteins including various transmembrane proteins of biological and pharmacological significance.
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Affiliation(s)
- Masaki Takahashi
- The institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Eri Sakota
- The institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshikazu Nakamura
- The institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; RIBOMIC Inc., Minato-ku, Tokyo 108-0071, Japan.
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17
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Specific Delivery of MiRNA for High Efficient Inhibition of Prostate Cancer by RNA Nanotechnology. Mol Ther 2016; 24:1267-77. [PMID: 27125502 DOI: 10.1038/mt.2016.85] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/07/2016] [Indexed: 12/19/2022] Open
Abstract
Both siRNA and miRNA can serve as powerful gene-silencing reagents but their specific delivery to cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miRNA seed-targeting sequence to block the growth of prostate cancer in mouse models. Utilizing the thermodynamically ultra-stable three-way junction of the pRNA of phi29 DNA packaging motor, RNA nanoparticles were constructed by bottom-up self-assembly containing the anti-prostate-specific membrane antigen (PSMA) RNA aptamer as a targeting ligand and anti-miR17 or anti-miR21 as therapeutic modules. The 16 nm RNase-resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection in mice and strongly bound to tumors with little or no accumulation in healthy organs 8 hours postinjection, and subsequently repressed tumor growth at low doses with high efficiency.
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18
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Catuogno S, Esposito CL, de Franciscis V. A trojan horse for human immunodeficiency virus. ACTA ACUST UNITED AC 2016; 22:313-4. [PMID: 25794434 DOI: 10.1016/j.chembiol.2015.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this issue of Chemistry & Biology, Zhou et al. demonstrate the possibility of effective multiple targeting of HIV infection by using a multifunctional molecule in which an anti-CCR5 receptor aptamer (G-3) is conjugated to an anti-TNPO3 siRNA.
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Affiliation(s)
- Silvia Catuogno
- Istituto di Endocrinologia ed Oncologia Sperimentale, CNR, 80145 Naples, Italy
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19
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Smooth Muscle Cell-targeted RNA Aptamer Inhibits Neointimal Formation. Mol Ther 2016; 24:779-87. [PMID: 26732878 DOI: 10.1038/mt.2015.235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/27/2015] [Indexed: 12/13/2022] Open
Abstract
Inhibition of vascular smooth muscle cell (VSMC) proliferation by drug eluting stents has markedly reduced intimal hyperplasia and subsequent in-stent restenosis. However, the effects of antiproliferative drugs on endothelial cells (EC) contribute to delayed re-endothelialization and late stent thrombosis. Cell-targeted therapies to inhibit VSMC remodeling while maintaining EC health are necessary to allow vascular healing while preventing restenosis. We describe an RNA aptamer (Apt 14) that functions as a smart drug by preferentially targeting VSMCs as compared to ECs and other myocytes. Furthermore, Apt 14 inhibits phosphatidylinositol 3-kinase/protein kinase-B (PI3K/Akt) and VSMC migration in response to multiple agonists by a mechanism that involves inhibition of platelet-derived growth factor receptor (PDGFR)-β phosphorylation. In a murine model of carotid injury, treatment of vessels with Apt 14 reduces neointimal formation to levels similar to those observed with paclitaxel. Importantly, we confirm that Apt 14 cross-reacts with rodent and human VSMCs, exhibits a half-life of ~300 hours in human serum, and does not elicit immune activation of human peripheral blood mononuclear cells. We describe a VSMC-targeted RNA aptamer that blocks cell migration and inhibits intimal formation. These findings provide the foundation for the translation of cell-targeted RNA therapeutics to vascular disease.
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20
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Lamberti I, Scarano S, Esposito CL, Antoccia A, Antonini G, Tanzarella C, De Franciscis V, Minunni M. In vitro selection of RNA aptamers against CA125 tumor marker in ovarian cancer and its study by optical biosensing. Methods 2015; 97:58-68. [PMID: 26542762 DOI: 10.1016/j.ymeth.2015.10.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/09/2015] [Accepted: 10/31/2015] [Indexed: 12/12/2022] Open
Abstract
Early identification of neoplastic diseases is essential to achieve timely therapeutic interventions and significantly reduce the mortality of patients. A well-known biomarker is the Cancer Antigen 125 (CA125) or 16 mucin (MUC 16), a glycoprotein of the human family of mucins, already used for the diagnostic and prognostic evaluation of ovarian cancer. Therefore, the detection of CA125 to now remains a promising tool in the early diagnosis of this tumor. In this paper, we describe the development of RNA aptamers that bind with high affinity the tumor antigen CA125. We performed eight cycles of selection against CA125 purified protein. The selected aptamers were cloned and sequenced and the binding properties of the most promising sequences were studied by Real Time PCR and Surface Plasmon Resonance (SPR) to evaluate their ability in targeting CA125 protein with perspective applications in aptamer-based bioassays.
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Affiliation(s)
- Ilaria Lamberti
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy
| | - Simona Scarano
- Università di Firenze, Dipartimento di Chimica "Ugo Schiff", Via della Lastruccia, 3-13, 50019 Sesto F.no (FI), Italy
| | - Carla Lucia Esposito
- Consiglio Nazionale delle Ricerche, Istituto per l'Endocrinologia e Oncologia Molecolare "G. Salvatore", Via T. De Amicis 95, 80131 Napoli, Italy
| | - Antonio Antoccia
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy; INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy
| | - Giovanni Antonini
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy; INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy
| | - Caterina Tanzarella
- Università di Roma Tre, Dipartimento di Scienze, Viale G. Marconi 446, 00146 Roma, Italy
| | - Vittorio De Franciscis
- Consiglio Nazionale delle Ricerche, Istituto per l'Endocrinologia e Oncologia Molecolare "G. Salvatore", Via T. De Amicis 95, 80131 Napoli, Italy.
| | - Maria Minunni
- INBB, Viale Medaglie d'oro 305, 00136 Roma, Italy; Università di Firenze, Dipartimento di Chimica "Ugo Schiff", Via della Lastruccia, 3-13, 50019 Sesto F.no (FI), Italy.
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21
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Yan M, Bai W, Zhu C, Huang Y, Yan J, Chen A. Design of nuclease-based target recycling signal amplification in aptasensors. Biosens Bioelectron 2015; 77:613-23. [PMID: 26485175 DOI: 10.1016/j.bios.2015.10.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Compared with conventional antibody-based immunoassay methods, aptasensors based on nucleic acid aptamer have made at least two significant breakthroughs. One is that aptamers are more easily used for developing various simple and rapid homogeneous detection methods by "sample in signal out" without multi-step washing. The other is that aptamers are more easily employed for developing highly sensitive detection methods by using various nucleic acid-based signal amplification approaches. As many substances playing regulatory roles in physiology or pathology exist at an extremely low concentration and many chemical contaminants occur in trace amounts in food or environment, aptasensors for signal amplification contribute greatly to detection of such targets. Among the signal amplification approaches in highly sensitive aptasensors, the nuclease-based target recycling signal amplification has recently become a research focus because it shows easy design, simple operation, and rapid reaction and can be easily developed for homogenous assay. In this review, we summarized recent advances in the development of various nuclease-based target recycling signal amplification with the aim to provide a general guide for the design of aptamer-based ultrasensitive biosensing assays.
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Affiliation(s)
- Mengmeng Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Chao Zhu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Yafei Huang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Jiao Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
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22
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Thiel WH, Thiel KW, Flenker KS, Bair T, Dupuy AJ, McNamara JO, Miller FJ, Giangrande PH. Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells. Methods Mol Biol 2015; 1218:187-99. [PMID: 25319652 DOI: 10.1007/978-1-4939-1538-5_11] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
After a decade of work to address cellular uptake, the principal obstacle to RNAi-based therapeutics, there is now well-deserved, renewed optimism about RNAi-based drugs. Phase I and II studies have shown safe, strong, and durable-gene knockdown (80-90%, lasting for a month after a single injection) and/or clinical benefit in treating several liver pathologies. Although promising, these studies have also highlighted the need for robust delivery techniques to develop RNAi therapeutics for treating other organ systems and diseases. Conjugation of siRNAs to cell-specific, synthetic RNA ligands (aptamers) is being proposed as a viable solution to this problem. While encouraging, the extended use of RNA aptamers as a delivery tool for siRNAs awaits the identification of RNA aptamer sequences capable of targeting and entering the cytoplasm of many different cell types. We describe a cell-based selection process for the rapid identification and characterization of RNA aptamers suited for delivering siRNA drugs into the cytoplasm of target cells. This process, termed "cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment)," entails the combination of multiple sophisticated technologies, including cell culture-based SELEX procedures, next-generation sequencing (NGS), and novel bioinformatics tools.
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Affiliation(s)
- William H Thiel
- Department of Internal Medicine, University of Iowa, 5202 MERF, 200 Hawkins Drive, Iowa City, IA, 52242, USA
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23
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Li H, Rychahou PG, Cui Z, Pi F, Evers BM, Shu D, Guo P, Luo W. RNA Nanoparticles Derived from Three-Way Junction of Phi29 Motor pRNA Are Resistant to I-125 and Cs-131 Radiation. Nucleic Acid Ther 2015; 25:188-97. [PMID: 26017686 DOI: 10.1089/nat.2014.0525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Radiation reagents that specifically target tumors are in high demand for the treatment of cancer. The emerging field of RNA nanotechnology might provide new opportunities for targeted radiation therapy. This study investigates whether chemically modified RNA nanoparticles derived from the packaging RNA (pRNA) three-way junction (3WJ) of phi29 DNA-packaging motor are resistant to potent I-125 and Cs-131 radiation, which is a prerequisite for utilizing these RNA nanoparticles as carriers for targeted radiation therapy. pRNA 3WJ nanoparticles were constructed and characterized, and the stability of these nanoparticles under I-125 and Cs-131 irradiation with clinically relevant doses was examined. RNA nanoparticles derived from the pRNA 3WJ targeted tumors specifically and they were stable under irradiation of I-125 and Cs-131 with clinically relevant doses ranging from 1 to 90 Gy over a significantly long time up to 20 days, while control plasmid DNA was damaged at 20 Gy or higher.
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Affiliation(s)
- Hui Li
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - Piotr G Rychahou
- 3 Department of Surgery, Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Zheng Cui
- 2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - Fengmei Pi
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - B Mark Evers
- 4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Dan Shu
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky.,4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Peixuan Guo
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky.,4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Wei Luo
- 5 Department of Radiation Medicine, Markey Cancer Center, University of Kentucky , Lexington, Kentucky
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24
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Goodwin S, Gade AM, Byrom M, Herrera B, Spears C, Anslyn EV, Ellington AD. Next-generation sequencing as input for chemometrics in differential sensing routines. Angew Chem Int Ed Engl 2015; 54:6339-42. [PMID: 25826754 PMCID: PMC4426058 DOI: 10.1002/anie.201501822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 12/21/2022]
Abstract
Differential sensing (DS) methods traditionally use spatially arrayed receptors and optical signals to create score plots from multivariate data which classify individual analytes or complex mixtures. Herein, a new approach is described, in which nucleic acid sequences and sequence counts are used as the multivariate data without the necessity of a spatial array. To demonstrate this approach to DS, previously selected aptamers, identified from the literature, were used as semi-specific receptors, Next-Gen DNA sequencing was used to generate data, and cell line differentiation was the test-bed application. The study of a principal component analysis loading plot revealed cross-reactivity between the aptamers. The technique generates high-dimensionality score plots, and should be applicable to any mixture of complex and subtly different analytes for which nucleic acid-based receptors exist.
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Affiliation(s)
- Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (USA)
| | - Alexandra M Gade
- Department of Chemistry A1590, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Michelle Byrom
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Baine Herrera
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Camille Spears
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA)
| | - Eric V Anslyn
- Department of Chemistry A1590, The University of Texas at Austin, Austin, TX 78712 (USA).
| | - Andrew D Ellington
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 (USA).
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25
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Chen A, Yang S. Replacing antibodies with aptamers in lateral flow immunoassay. Biosens Bioelectron 2015; 71:230-242. [PMID: 25912679 DOI: 10.1016/j.bios.2015.04.041] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 12/30/2022]
Abstract
Aptamers have been identified against various targets as a type of chemical or nucleic acid ligand by systematic evolution of ligands by exponential enrichment (SELEX) with high sensitivity and specificity. Aptamers show remarkable advantages over antibodies due to the nucleic acid nature and target-induced structure-switching properties and are widely used to design various fluorescent, electrochemical, or colorimetric biosensors. However, the practical applications of aptamer-based sensing and diagnostics are still lagging behind those of antibody-based tests. Lateral flow immunoassay (LFIA) represents a well established and appropriate technology among rapid assays because of its low cost and user-friendliness. The antibody-based platform is utilized to detect numerous targets, but it is always hampered by the antibody preparation time, antibody stability, and effect of modification on the antibody. Seeking alternatives to antibodies is an area of active research and is of tremendous importance. Aptamers are receiving increasing attention in lateral flow applications because of a number of important potential performance advantages. We speculate that aptamer-based LFIA may be one of the first platforms for commercial use of aptamer-based diagnosis. This review first gives an introduction to aptamer including the selection process SELEX with its focus on aptamer advantages over antibodies, and then depicts LFIA with its focus on aptamer opportunities in LFIA over antibodies. Furthermore, we summarize the recent advances in the development of aptamer-based lateral flow biosensing assays with the aim to provide a general guide for the design of aptamer-based lateral flow biosensing assays.
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Affiliation(s)
- Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
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26
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Rohde JH, Weigand JE, Suess B, Dimmeler S. A Universal Aptamer Chimera for the Delivery of Functional microRNA-126. Nucleic Acid Ther 2015; 25:141-51. [PMID: 25844955 DOI: 10.1089/nat.2014.0501] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
microRNAs (miRs) regulate vascular diseases such as atherosclerosis and cancer. miR-126 is important for endothelial cell signaling and promotes angiogenesis, protects against atherosclerosis, and reduces breast cancer cell growth and metastasis. The overexpression of miR-126, therefore, may be an attractive therapeutic strategy for the treatment of cardiovascular disease or cancer. Here we report a novel strategy to deliver miR-126 to endothelial and breast cancer cells. We tested three different strategies to deliver miR-126 by linking the miR to an aptamer for the ubiquitously expressed transferrin receptor (transferrin receptor aptamer, TRA). Linking the precursor of miR-126 (pre-miR-126) to the TRA by annealing of a complementary stick led to efficient uptake and processing of miR-126, resulting in the delivery of 1.6×10(6)±0.3×10(6) copies miR-126-3p per ng RNA in human endothelial cells and 7.4×10(5)±2×10(5) copies miR-126-3p per ng in MCF7 breast cancer cells. The functionality of the active TRA-miR-126 chimera was further demonstrated by showing that the chimera represses the known miR-126 target VCAM-1 and improved endothelial cell sprouting in a spheroid assay. Moreover, the TRA-miR-126 chimera reduced proliferation and paracrine endothelial cell recruitment of breast cancer cells to a similar extent as miR-126-3p mimics introduced by conventional liposome-based transfection. Together, this data demonstrates that pre-miR-126 can be delivered by a non-specific aptamer to exert biological functions in two different cell models. The use of the TRA-miR-126 chimera or the combination of the delivery strategy with other endothelial or tumor specific aptamers may provide an interesting therapeutic option to treat vascular disease or cancers.
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Affiliation(s)
- Jan-H Rohde
- 1Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Julia E Weigand
- 2Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- 2Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Stefanie Dimmeler
- 1Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany.,3German Centre for Cardiovascular Research (DZHK), RheinMain, Frankfurt, Germany
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27
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Goodwin S, Gade AM, Byrom M, Herrera B, Spears C, Anslyn EV, Ellington AD. Next-Generation Sequencing as Input for Chemometrics in Differential Sensing Routines. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Cell-specific RNA aptamer against human CCR5 specifically targets HIV-1 susceptible cells and inhibits HIV-1 infectivity. ACTA ACUST UNITED AC 2015; 22:379-90. [PMID: 25754473 DOI: 10.1016/j.chembiol.2015.01.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/29/2014] [Accepted: 01/25/2015] [Indexed: 11/21/2022]
Abstract
The C-C chemokine receptor type 5 (CCR5) is a receptor expressed by T cells and macrophages that serves as a coreceptor for macrophage-tropic HIV-1. Loss of CCR5 is associated with resistance to HIV-1. Here, we combine the live-cell-based SELEX with high-throughput sequencing technology to generate CCR5 RNA aptamers capable of specifically targeting HIV-1 susceptible cells (as small interfering RNA [siRNA] delivery agent) and inhibiting HIV-1 infectivity (as antiviral agent) via block of the CCR5 required for HIV-1 to enter cells. One of the best candidates, G-3, efficiently bound and was internalized into human CCR5-expressing cells. The G-3 specifically neutralized R5 virus infection in primary peripheral blood mononuclear cells, and in vivo generated human CD4(+) T cells with a nanomolar inhibitory concentration 50%. G-3 was also capable of transferring functional siRNAs to CCR5-expressing cells. Collectively, the cell-specific, internalizing, CCR5-targeted aptamers and aptamer-siRNA conjugates offer promise for overcoming some of the current challenges of drug resistance in HIV-1 by providing cell-type- or tissue-specific delivery of various therapeutic moieties.
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29
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Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e201. [PMID: 25291143 PMCID: PMC4217074 DOI: 10.1038/mtna.2014.49] [Citation(s) in RCA: 341] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.
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Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity. Biochem Biophys Res Commun 2014; 453:681-5. [PMID: 25242523 DOI: 10.1016/j.bbrc.2014.09.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/06/2014] [Indexed: 01/01/2023]
Abstract
Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher's attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with Kd 56±7.3nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy.
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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Yan A, Levy M. Cell internalization SELEX: in vitro selection for molecules that internalize into cells. Methods Mol Biol 2014; 1103:241-65. [PMID: 24318899 DOI: 10.1007/978-1-62703-730-3_18] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aptamer technology allows for the selection of nucleic acids that can bind to and enter cells. By establishing conditions during the selection that eliminate cell-surface binders as well as non-internalizing RNAs, only extremely tightly bound aptamers or aptamers that have internalized are recovered. We describe a general scheme for selecting RNA molecules that are capable of internalizing into cells and discuss the factors that can affect a successful selection. Much like standard cell-surface selections, these types of selections should be possible independent of detailed knowledge of the cell surface.
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Affiliation(s)
- Amy Yan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
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Kim EY, Kim JW, Kim WK, Han BS, Park SG, Chung BH, Lee SC, Bae KH. Selection of aptamers for mature white adipocytes by cell SELEX using flow cytometry. PLoS One 2014; 9:e97747. [PMID: 24844710 PMCID: PMC4028271 DOI: 10.1371/journal.pone.0097747] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/23/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Adipose tissue, mainly composed of adipocytes, plays an important role in metabolism by regulating energy homeostasis. Obesity is primarily caused by an abundance of adipose tissue. Therefore, specific targeting of adipose tissue is critical during the treatment of obesity, and plays a major role in overcoming it. However, the knowledge of cell-surface markers specific to adipocytes is limited. METHODS AND RESULTS We applied the CELL SELEX (Systematic Evolution of Ligands by EXponential enrichment) method using flow cytometry to isolate molecular probes for specific recognition of adipocytes. The aptamer library, a mixture of FITC-tagged single-stranded random DNAs, is used as a source for acquiring molecular probes. With the increasing number of selection cycles, there was a steady increase in the fluorescence intensity toward mature adipocytes. Through 12 rounds of SELEX, enriched aptamers showing specific recognition toward mature 3T3-L1 adipocyte cells were isolated. Among these, two aptamers (MA-33 and 91) were able to selectively bind to mature adipocytes with an equilibrium dissociation constant (Kd) in the nanomolar range. These aptamers did not bind to preadipocytes or other cell lines (such as HeLa, HEK-293, or C2C12 cells). Additionally, it was confirmed that MA-33 and 91 can distinguish between mature primary white and primary brown adipocytes. CONCLUSIONS These selected aptamers have the potential to be applied as markers for detecting mature white adipocytes and monitoring adipogenesis, and could emerge as an important tool in the treatment of obesity.
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Affiliation(s)
- Eun Young Kim
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
| | - Ji Won Kim
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, Republic of Korea
| | - Won Kon Kim
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
| | - Baek Soo Han
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
| | - Sung Goo Park
- Medical Proteomics Research Center, KRIBB, Daejeon, Republic of Korea
| | - Bong Hyun Chung
- BioNanotechnology Research Center, Bioconvergence Research Institute, KRIBB, Daejeon, Republic of Korea
| | - Sang Chul Lee
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, Republic of Korea
| | - Kwang-Hee Bae
- Research Center for Integrated Cellulomics, KRIBB, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology (UST) of Korea, Daejeon, Republic of Korea
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Binzel DW, Khisamutdinov EF, Guo P. Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments. Biochemistry 2014; 53:2221-31. [PMID: 24694349 PMCID: PMC4004221 DOI: 10.1021/bi4017022] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The
emerging field of RNA nanotechnology necessitates creation
of functional RNA nanoparticles but has been limited by particle instability.
It has been shown that the three-way junction of bacteriophage phi29
motor pRNA has unusual stability and can self-assemble from three
fragments with high efficiency. It is generally believed that RNA
and DNA folding is energy landscape-dependent, and the folding of
RNA is driven by enthalpy. Here we examine the thermodynamic characteristics
of the 3WJ components as 2′-fluoro RNA, DNA, and RNA. It was
seen that the three fragments existed either in 3WJ complex or as
monomers, with the intermediate of dimers almost undetectable. It
seems that the three fragments can lead to the formation of the 3WJ
complex efficiently within a rapid time. A low dissociation constant
(apparent KD) of 11.4 nM was determined
for RNA, inclusion of 2′-F pyrimidines strengthened the KD to 4.5 nM, and substitution of DNA weakened
it to 47.7 nM. The ΔG°37, were
−36, −28, and −15 kcal/mol for 3WJ2′-F, 3WJRNA, and 3WJDNA, respectively. It is found
that the formation of the three-component complex was governed by
entropy, instead of enthalpy, as usually found in RNA complexes.
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Affiliation(s)
- Daniel W Binzel
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, United States
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Yang M, Jiang G, Li W, Qiu K, Zhang M, Carter CM, Al-Quran SZ, Li Y. Developing aptamer probes for acute myelogenous leukemia detection and surface protein biomarker discovery. J Hematol Oncol 2014; 7:5. [PMID: 24405684 PMCID: PMC3895837 DOI: 10.1186/1756-8722-7-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 12/24/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The majority of patients with acute myelogenous leukemia (AML) still die of their disease. In order to improve survival rates in AML patients, new strategies are necessary to discover biomarkers for the detection and targeted therapy of AML. One of the advantages of the aptamer-based technology is the unique cell-based selection process, which allows us to efficiently select for cell-specific aptamers without knowing which target molecules are present on the cell surface. METHODS The NB4 AML cell line was used as the target cell population for selecting single stranded DNA aptamers. After determining the affinity of selected aptamers to leukocytes, the aptamers were used to phenotype human bone marrow leukocytes and AML cells in clinical specimens. Then a biotin-labelled aptamer was used to enrich and identify its target surface protein. RESULTS Three new aptamers were characterized from the selected aptamer pools (JH6, JH19, and K19). All of them can selectively recognize myeloid cells with Kd in the low nanomole range (2.77 to 12.37 nM). The target of the biotin-labelled K19 aptamer probe was identified as Siglec-5, a surface membrane protein in low abundance whose expression can serve as a biomarker of granulocytic maturation and be used to phenotype AML. More importantly, Siglec-5 expression can be used to detect low concentrations of AML cells in human bone marrow specimens, and functions as a potential target for leukemic therapy. CONCLUSIONS We have demonstrated a pipeline approach for developing single stranded DNA aptamer probes, phenotyping AML cells in clinical specimens, and then identifying the aptamer-recognized target protein. The developed aptamer probes and identified Siglec-5 protein may potentially be used for leukemic cell detection and therapy in our future clinical practice.
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MESH Headings
- Acute Disease
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation, Myelomonocytic/genetics
- Antigens, Differentiation, Myelomonocytic/metabolism
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Diagnosis, Differential
- Flow Cytometry
- HL-60 Cells
- Humans
- Lectins/genetics
- Lectins/metabolism
- Leukemia, Myeloid/diagnosis
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/pathology
- Leukocytes/metabolism
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Polymerase Chain Reaction
- Protein Binding
- Reproducibility of Results
- SELEX Aptamer Technique/methods
- Sensitivity and Specificity
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Affiliation(s)
- Mingli Yang
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Guohua Jiang
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Wenjing Li
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Kai Qiu
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Min Zhang
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Christopher M Carter
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Samer Z Al-Quran
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
| | - Ying Li
- UF/Shands Medical Laboratory at Rocky Point, 4800 35th Drive, Gainesville, FL 32608, USA
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Davydova AS, Vorobjeva MA, Zenkova MA, Silnikov VN, François JC, Venyaminova AG. New cellular RNA elimination method for cell-based SELEX of modified RNA aptamers. Mol Biol 2013. [DOI: 10.1134/s0026893313060034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Identification of RNA aptamers that internalize into HPV-16 E6/E7 transformed tonsillar epithelial cells. Virology 2013; 446:325-33. [PMID: 24074596 DOI: 10.1016/j.virol.2013.08.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 06/20/2013] [Accepted: 08/14/2013] [Indexed: 01/09/2023]
Abstract
Human papillomavirus type 16 (HPV-16) associated oropharyngeal cancers are on a significant increase and better therapeutic strategies are needed. The HPV-16 oncogenes E6 and E7 are expressed in HPV-associated cancers and are able to transform human tonsillar epithelial cells (HTECs). We used cell-Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select for RNA aptamers that entered into HPV-16 E6/E7-HTECs. After 12 rounds of cell-SELEX, a pool of aptamers was obtained that had significantly greater internalization capacity (~5-fold) into E6/E7-HTECs as compared to primary HTECs or fibroblasts. Analysis of individual aptamers from the pool indicated variable internalization into E6/E7-HTECs (1-8-fold as compared to a negative control). Most of the individual aptamers internalized into E6/E7 and primary HTECs with similar efficiency, while one aptamer exhibited ~3-fold better internalization into E6/E7-HTECs. Aptamers that internalize into cells may be useful for delivering therapeutic agents to HPV-16 associated malignancies.
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Conidi A, van den Berghe V, Huylebroeck D. Aptamers and their potential to selectively target aspects of EGF, Wnt/β-catenin and TGFβ-smad family signaling. Int J Mol Sci 2013; 14:6690-719. [PMID: 23531534 PMCID: PMC3645661 DOI: 10.3390/ijms14046690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/05/2013] [Accepted: 03/12/2013] [Indexed: 02/07/2023] Open
Abstract
The smooth identification and low-cost production of highly specific agents that interfere with signaling cascades by targeting an active domain in surface receptors, cytoplasmic and nuclear effector proteins, remain important challenges in biomedical research. We propose that peptide aptamers can provide a very useful and new alternative for interfering with protein–protein interactions in intracellular signal transduction cascades, including those emanating from activated receptors for growth factors. By their targeting of short, linear motif type of interactions, peptide aptamers have joined nucleic acid aptamers for use in signaling studies because of their ease of production, their stability, their high specificity and affinity for individual target proteins, and their use in high-throughput screening protocols. Furthermore, they are entering clinical trials for treatment of several complex, pathological conditions. Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, starting with the published as well as potential applications of aptamers targeting Epidermal Growth Factor Receptor signaling. We then discuss the opportunities for using aptamers in other complex pathways, including Wnt/β-catenin, and focus on Transforming Growth Factor-β/Smad family signaling.
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Affiliation(s)
- Andrea Conidi
- Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Campus Gasthuisberg, Building Ond & Nav4 p.o.box 812, room 05.313, Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium.
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Mease RC, Foss CA, Pomper MG. PET imaging in prostate cancer: focus on prostate-specific membrane antigen. Curr Top Med Chem 2013. [PMID: 23590171 DOI: 10.2174/092986712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Prostate cancer (PCa) is the second leading cause of cancer-related death in American men. Positron emission tomography/computed tomography (PET/CT) with emerging radiopharmaceuticals promises accurate staging of primary disease, restaging of recurrent disease, detection of metastatic lesions and, ultimately, for predicting the aggressiveness of disease. Prostate-specific membrane antigen (PSMA) is a well-characterized imaging biomarker of PCa. Because PSMA levels are directly related to androgen independence, metastasis and progression, PSMA could prove an important target for the development of new radiopharmaceuticals for PET. Preclinical data for new PSMA-based radiotracers are discussed and include new (89)Zr- and (64)Cu-labeled anti-PSMA antibodies and antibody fragments, (64)Cu-labeled aptamers, and (11)C-, (18)F-, (68)Ga-, (64)Cu-, and (86)Y-labeled low molecular weight inhibitors of PSMA. Several of these agents, namely (68)Ga- HBED-CC conjugate 15, (18)F-DCFBC 8, and BAY1075553 are particularly promising, each having detected sites of PCa in initial clinical studies. These early clinical results suggest that PET/CT using PSMA-targeted agents, especially with compounds of low molecular weight, will make valuable contributions to the management of PCa.
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Affiliation(s)
- Ronnie C Mease
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical School, Baltimore, MD 21287, USA
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Ray P, Cheek MA, Sharaf ML, Li N, Ellington AD, Sullenger BA, Shaw BR, White RR. Aptamer-mediated delivery of chemotherapy to pancreatic cancer cells. Nucleic Acid Ther 2012; 22:295-305. [PMID: 23030589 PMCID: PMC3464421 DOI: 10.1089/nat.2012.0353] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/11/2012] [Indexed: 01/05/2023] Open
Abstract
Gemcitabine is a nucleoside analog that is currently the best available single-agent chemotherapeutic drug for pancreatic cancer. However, efficacy is limited by our inability to deliver sufficient active metabolite into cancer cells without toxic effects on normal tissues. Targeted delivery of gemcitabine into cancer cells could maximize effectiveness and concurrently minimize toxic side effects by reducing uptake into normal cells. Most pancreatic cancers overexpress epidermal growth factor receptor (EGFR), a trans-membrane receptor tyrosine kinase. We utilized a nuclease resistant RNA aptamer that binds and is internalized by EGFR on pancreatic cancer cells to deliver gemcitabine-containing polymers into EGFR-expressing cells and inhibit cell proliferation in vitro. This approach to cell type-specific therapy can be adapted to other targets and to other types of therapeutic cargo.
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Affiliation(s)
- Partha Ray
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Marcus A. Cheek
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Mariam L. Sharaf
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Na Li
- Department of Chemistry & Biochemistry, The University of Texas at Austin, Austin, Texas
| | - Andrew D. Ellington
- Department of Chemistry & Biochemistry, The University of Texas at Austin, Austin, Texas
| | - Bruce A. Sullenger
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | | | - Rebekah R. White
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
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Jiang G, Zhang M, Yue B, Yang M, Carter C, Al-Quran SZ, Li B, Li Y. PTK7: a new biomarker for immunophenotypic characterization of maturing T cells and T cell acute lymphoblastic leukemia. Leuk Res 2012; 36:1347-53. [PMID: 22898210 DOI: 10.1016/j.leukres.2012.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 06/30/2012] [Accepted: 07/02/2012] [Indexed: 10/28/2022]
Abstract
Protein tyrosine kinase-7 (PTK7) was recently identified as a surface protein expressed on hematopoietic cells. To determine if PTK7 is a useful biomarker in clinical practice for acute leukemia immunophenotyping and detection, we examined the PTK7 expression in human bone marrow and thymic specimens. Our results show that PTK7 expression in normal thymic T cells is tightly regulated during the maturational process, but in T cell acute lymphoblastic leukemia (T-ALL) the expected temporal relationship of expression between PTK7 and other maturational T cell markers is lost or disrupted. In addition, nearly all T-ALL cases expressed higher PTK7 levels than mature T cells in the human bone marrow specimens. Therefore, in conjunction with other T cell markers, PTK7 has utility as a biomarker for detecting minimal residual disease of T-ALL in the bone marrow.
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Affiliation(s)
- Guohua Jiang
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, United States
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42
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Foss CA, Mease RC, Cho SY, Kim HJ, Pomper MG. GCPII imaging and cancer. Curr Med Chem 2012; 19:1346-59. [PMID: 22304713 DOI: 10.2174/092986712799462612] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/26/2011] [Accepted: 12/27/2011] [Indexed: 12/11/2022]
Abstract
Glutamate carboxypeptidase II (GCPII) in the central nervous system is referred to as the prostate-specific membrane antigen (PSMA) in the periphery. PSMA serves as a target for imaging and treatment of prostate cancer and because of its expression in solid tumor neovasculature has the potential to be used in this regard for other malignancies as well. An overview of GCPII/PSMA in cancer, as well as a discussion of imaging and therapy of prostate cancer using a wide variety of PSMA-targeting agents is provided.
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Affiliation(s)
- C A Foss
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical School, Baltimore, MD 21231, USA
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Nucleic acids in human glioma treatment: innovative approaches and recent results. JOURNAL OF SIGNAL TRANSDUCTION 2012; 2012:735135. [PMID: 22685651 PMCID: PMC3364599 DOI: 10.1155/2012/735135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 02/29/2012] [Indexed: 02/08/2023]
Abstract
Gliomas are the most common primary central nervous system tumors with a dismal prognosis. Despite recent advances in surgery, radiotherapy, and chemotherapy, current treatment regimens have a modest survival benefit. A crucial challenge is to deliver drugs effectively to invasive glioma cells residing in a sanctuary within the central nervous system. New therapies are essential, and oligonucleotide-based approaches, including antisense, microRNAs, small interfering RNAs, and nucleic acid aptamers, may provide a viable strategy. Thanks to their unique characteristics (low size, good affinity for the target, no immunogenicity, chemical structures that can be easily modified to improve their in vivo applications), these molecules may represent a valid alternative to antibodies particularly to overcome challenges presented by the blood-brain barrier. Here we will discuss recent results on the use of oligonucleotides that will hopefully provide new effective treatment for gliomas.
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Minicells: Versatile vectors for targeted drug or si/shRNA cancer therapy. Curr Opin Biotechnol 2011; 22:909-16. [DOI: 10.1016/j.copbio.2011.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/14/2011] [Indexed: 02/03/2023]
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Esposito CL, Passaro D, Longobardo I, Condorelli G, Marotta P, Affuso A, de Franciscis V, Cerchia L. A neutralizing RNA aptamer against EGFR causes selective apoptotic cell death. PLoS One 2011; 6:e24071. [PMID: 21915281 PMCID: PMC3167817 DOI: 10.1371/journal.pone.0024071] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/29/2011] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers have been developed as high-affinity ligands that may act as antagonists of disease-associated proteins. Aptamers are non immunogenic and characterised by high specificity and low toxicity thus representing a valid alternative to antibodies or soluble ligand receptor traps/decoys to target specific cancer cell surface proteins in clinical diagnosis and therapy. The epidermal growth factor receptor (EGFR) has been implicated in the development of a wide range of human cancers including breast, glioma and lung. The observation that its inhibition can interfere with the growth of such tumors has led to the design of new drugs including monoclonal antibodies and tyrosine kinase inhibitors currently used in clinic. However, some of these molecules can result in toxicity and acquired resistance, hence the need to develop novel kinds of EGFR-targeting drugs with high specificity and low toxicity. Here we generated, by a cell-Systematic Evolution of Ligands by EXponential enrichment (SELEX) approach, a nuclease resistant RNA-aptamer that specifically binds to EGFR with a binding constant of 10 nM. When applied to EGFR-expressing cancer cells the aptamer inhibits EGFR-mediated signal pathways causing selective cell death. Furthermore, at low doses it induces apoptosis even of cells that are resistant to the most frequently used EGFR-inhibitors, such as gefitinib and cetuximab, and inhibits tumor growth in a mouse xenograft model of human non-small-cell lung cancer (NSCLC). Interestingly, combined treatment with cetuximab and the aptamer shows clear synergy in inducing apoptosis in vitro and in vivo. In conclusion, we demonstrate that this neutralizing RNA-aptamer is a promising bio-molecule that can be developed as a more effective alternative to the repertoire of already existing EGFR-inhibitors.
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Affiliation(s)
- Carla Lucia Esposito
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR “G. Salvatore”, Naples, Italy
| | - Diana Passaro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, University of Naples “Federico II”, Naples, Italy
| | - Immacolata Longobardo
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, University of Naples “Federico II”, Naples, Italy
| | - Gerolama Condorelli
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR “G. Salvatore”, Naples, Italy
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, University of Naples “Federico II”, Naples, Italy
- Facoltà di Scienze Biotecnologiche, University of Naples “Federico II”, Naples, Italy
| | - Pina Marotta
- Animal Model Facility, Biogem s.c.a.r.l., Ariano Irpino, Avellino, Italy
| | - Andrea Affuso
- Animal Model Facility, Biogem s.c.a.r.l., Ariano Irpino, Avellino, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Vittorio de Franciscis
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR “G. Salvatore”, Naples, Italy
| | - Laura Cerchia
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR “G. Salvatore”, Naples, Italy
- * E-mail:
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46
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Aptamer–biotin–streptavidin–C1q complexes can trigger the classical complement pathway to kill cancer cells. In Vitro Cell Dev Biol Anim 2011; 46:107-13. [PMID: 19915929 DOI: 10.1007/s11626-009-9257-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 10/22/2009] [Indexed: 01/11/2023]
Abstract
Nucleic acid aptamers are regarded as rivals for antibodies and as such are being investigated for their therapeutic potential. In the present work, it is shown that two different high-affinity DNA aptamers developed previously by Ferreira et al. against MUC1 antigen (designated MUC1-5TR-1 and MUC1-S1.3/S2.2) on MCF7 breast cancer cells can be linked to the first component of complement (C1q) via a biotin–streptavidin system and induce significant killing of MCF7 cells in vitro. Cell viability was assessed by Trypan blue uptake and absorbance at 590 nm of stained cells following buffer washes and lysis in 1% SDS. While the killing effect is demonstrable versus various controls, dependent on aptamer dose, and reproducible, it appears to kill maximally about half of treated MCF7 cells. Possible reasons for the marginal killing effect include antigenic shedding in vitro and membrane-bound complement regulatory proteins (mCRPs) on the cell surface such as CD46, CD55, and CD59 which act to inhibit complement-mediated lysis of cells. Future in vitro research could benefit from application of mCRP-specific aptamers in combination with anti-MUC1 aptamers to overcome surface protective mechanisms while attacking the plasma membrane of MCF7 cells or other MUC1-expressing cancer cells. However, in vivo such a combination could have deleterious effects on normal MUC1-expressing cells as well.
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47
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Abstract
Aptamers that target a specific cell subpopulation within composite mixtures represent invaluable tools in biomedical research and in the development of cell-specific therapeutics. Here we describe a detailed protocol for a modular and generally applicable scheme to select aptamers that target the subpopulations of cells in which you are interested. A fluorescence-activated cell-sorting device is used to simultaneously differentiate and separate those subpopulations of cells having bound and unbound aptamers. There are fewer false positives when using this approach in comparison with other cell-selection approaches in which unspecific binding of nucleic acids to cells with reduced membrane integrity or their unselective uptake by dead cells occurs more often. The protocol provides a state-of-the-art approach for identifying aptamers that selectively target virtually any cell type under investigation. As an example, we provide the step-by-step protocol targeting CD19(+) Burkitt's lymphoma cells, starting from the pre-SELEX (systematic evolution of ligands by exponential amplification) measurements to establish suitable SELEX conditions and ending at completion of the SELEX procedure, which reveals the enriched single-stranded DNA library.
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48
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Ahn JY, Lee SW, Kang HS, Jo M, Lee DK, Laurell T, Kim S. Aptamer microarray mediated capture and mass spectrometry identification of biomarker in serum samples. J Proteome Res 2010; 9:5568-73. [PMID: 20806970 DOI: 10.1021/pr100300t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sensitive detection of molecular biomarkers in clinical samples is crucially important in disease diagnostics. This paper reports the development of an aptamer microarray platform combined with sol-gel technology to identify low-abundance targets in complex serum samples. Because of the nanoporous structure of the sol-gel, a high capacity to immobilize the affinity specific aptamers is accomplished which allows binding and detection of target molecules with high sensitivity. The captured protein is digested in situ and the obtained digest was analyzed by ESI-MS without any interference from the affinity probe. TBP (TATA Box Protein) and its specific aptamers were chosen as a model system. A proof of concept with protein concentrations ranging between nanomolar to micromolar is reported, showing a good linearity up to 400 nM when characterized in an aptamer sandwich assay. Moreover, as low as 0.001% of target protein present in total serum proteins could be identified without any pretreatment step using ESI MS/MS mass spectrometry. We believe this novel strategy could become an efficient method for aptamer-based biomarker detection linked directly to mass spectrometry readout.
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Affiliation(s)
- Ji-Young Ahn
- Department of Biomedical Engineering, Dongguk University, Joong-Gu, Seoul, 100-715, Korea
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49
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Targeting cancer cells with nucleic acid aptamers. Trends Biotechnol 2010; 28:517-25. [PMID: 20719399 DOI: 10.1016/j.tibtech.2010.07.005] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/12/2010] [Accepted: 07/15/2010] [Indexed: 01/11/2023]
Abstract
Aptamers are short, structured, single-stranded RNA or DNA ligands that bind with high affinity to their target molecules, which range from small chemicals to large cell-surface and transmembrane proteins. Aptamers are now emerging as promising molecules to target specific cancer epitopes in clinical diagnosis and therapy. Furthermore, because of their high specificity and low toxicity, aptamers might be considered as the compounds-of-choice for in vivo cell recognition. Specific cancer cell recognition could be capitalized upon for delivering therapeutic nanoparticles, small interfering RNA bioconjugates, chemotherapeutic cargos or molecular imaging probes. In this article, we review recent advances in the use of aptamers for in vivo cancer cell recognition, with a particular focus on novel applications of aptamers for targeting the cell surface.
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50
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Abstract
Aptamers are single-stranded oligonucleotides that fold into defined architectures and bind to targets such as proteins. In binding proteins they often inhibit protein–protein interactions and thereby may elicit therapeutic effects such as antagonism. Aptamers are discovered using SELEX (systematic evolution of ligands by exponential enrichment), a directed in vitro evolution technique in which large libraries of degenerate oligonucleotides are iteratively and alternately partitioned for target binding. They are then amplified enzymatically until functional sequences are identified by the sequencing of cloned individuals. For most therapeutic purposes, aptamers are truncated to reduce synthesis costs, modified at the sugars and capped at their termini to increase nuclease resistance, and conjugated to polyethylene glycol or another entity to reduce renal filtration rates. The first aptamer approved for a therapeutic application was pegaptanib sodium (Macugen; Pfizer/Eyetech), which was approved in 2004 by the US Food and Drug Administration for macular degeneration. Eight other aptamers are currently undergoing clinical evaluation for various haematology, oncology, ocular and inflammatory indications. Aptamers are ultimately chemically synthesized in a readily scalable process in which specific conjugation points are introduced with defined stereochemistry. Unlike some protein therapeutics, aptamers do not elicit antibodies, and because aptamers generally contain sugars modified at their 2′-positions, Toll-like receptor-mediated innate immune responses are also abrogated. As aptamers are oligonucleotides they can be readily assembled into supramolecular multi-component structures using hybridization. Owing to the fact that binding to appropriate cell-surface targets can lead to internalization, aptamers can also be used to deliver therapeutic cargoes such as small interfering RNA. Supramolecular assemblies of aptamers and delivery agents have already been demonstrated in vivo and may pave the way for further therapeutic strategies with this modality in the future.
Aptamers are oligonucleotide sequences that are capable of recognizing target proteins with an affinity and specificity rivalling that of antibodies. In this article, Keefe and colleagues discuss the development, properties and therapeutic potential of aptamers, highlighting those currently in the clinic. Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Aptamers exhibit significant advantages relative to protein therapeutics in terms of size, synthetic accessibility and modification by medicinal chemistry. Despite these properties, aptamers have been slow to reach the marketplace, with only one aptamer-based drug receiving approval so far. A series of aptamers currently in development may change how nucleic acid therapeutics are perceived. It is likely that in the future, aptamers will increasingly find use in concert with other therapeutic molecules and modalities.
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