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Sun W, Zhang H, Xie W, Ma L, Dang Y, Liu Y, Li L, Qu F, Tan W. Development of Integrin-Facilitated Bispecific Aptamer Chimeras for Membrane Protein Degradation. J Am Chem Soc 2024; 146:25490-25500. [PMID: 39226482 DOI: 10.1021/jacs.4c04794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The emergence of lysosome-targeting chimeras (LYTACs), which represents a promising strategy for membrane protein degradation based on lysosomal pathways, has attracted much attention in disease intervention and treatment. However, the expression level of commonly used lysosome-targeting receptors (LTRs) varies in different cell lines, thus limiting the broad applications of LYTACs. To overcome this difficulty, we herein report the development of integrin α3β1 (ITGA3B1)-facilitated bispecific aptamer chimeras (ITGBACs) as a platform for the degradation of membrane proteins. ITGBACs consist of two aptamers, one targeting ITGA3B1 and another binding to the membrane-associated protein of interest (POI), effectively transporting the POI into lysosomes for degradation. Our findings demonstrate that ITGBACs effectively eliminate pathological membrane proteins, such as CD71 and PTK7, inducing significant cell-cycle arrest and apoptosis and markedly inhibiting tumor growth in tumor-bearing mice models. Therefore, this work provides a novel and versatile membrane protein degradation platform, offering a promising targeted therapy based on tumor-specific LTRs.
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Affiliation(s)
- Weidi Sun
- 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
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Hui Zhang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China
| | - Wanlin Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lele Ma
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Dang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yuan Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China
| | - Ling Li
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Fengli Qu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, Zhejiang 310024, China
| | - Weihong Tan
- 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
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Uinarni H, Oghenemaro EF, Menon SV, Hjazi A, Ibrahim FM, Kaur M, Zafarjonovna AZ, Deorari M, Jabir MS, Zwamel AH. Breaking Barriers: Nucleic Acid Aptamers in Gastrointestinal (GI) Cancers Therapy. Cell Biochem Biophys 2024; 82:1763-1776. [PMID: 38916791 DOI: 10.1007/s12013-024-01367-w] [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] [Accepted: 06/13/2024] [Indexed: 06/26/2024]
Abstract
Conventional cancer therapies can have significant adverse effects as they are not targeted to cancer cells and may damage healthy cells. Single-stranded oligonucleotides assembled in a particular architecture, known as aptamers, enable them to attach selectively to target areas. Usually, they are created by Systematic Evolution of Ligand by Exponential enrichment (SELEX), and they go through a rigorous pharmacological revision process to change their therapeutic half-life, affinity, and specificity. They could thus offer a viable substitute for antibodies in the targeted cancer treatment market. Although aptamers can be a better choice in some situations, antibodies are still appropriate for many other uses. The technique of delivering aptamers is simple and reasonable, and the time needed to manufacture them is relatively brief. Aptamers do not require animals or an immune response to be produced, in contrast to antibodies. When used as a medication, aptamers can directly suppress tumor cells. As an alternative, they can be included in systems for targeted drug delivery that administer medications specifically to tumor cells while reducing toxicity to healthy cells. The most recent and cutting-edge methods for treating gastrointestinal (GI) tract cancer with aptamers will be covered in this review, with a focus on targeted therapy as a means of conquering resistance to traditional medicines.
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Affiliation(s)
- Herlina Uinarni
- Department of Anatomy, School of Medicine and Health Sciences Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia.
- Radiology department of Pantai Indah Kapuk Hospital Jakarta, Jakarta, Indonesia.
| | - Enwa Felix Oghenemaro
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Delta State University, Abraka, Delta State, Nigeria
| | - Soumya V Menon
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Fatma Magdi Ibrahim
- Assisstant professor, Community Health Nursing, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE
- Lecturer, geriatric nursing, Mansoura University, Mansoura, Egypt
| | - Mandeep Kaur
- Department of Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | | | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Majid S Jabir
- Department of applied sciences, University of technology, Baghdad, Iraq
| | - Ahmed Hussein Zwamel
- Medical laboratory technique college, the Islamic University, Najaf, Iraq
- Medical laboratory technique college, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- Medical laboratory technique college, the Islamic University of Babylon, Babylon, Iraq
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3
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Zheng L, Li J, Li Y, Sun W, Ma L, Qu F, Tan W. Empowering Exosomes with Aptamers for Precision Theranostics. SMALL METHODS 2024:e2400551. [PMID: 38967170 DOI: 10.1002/smtd.202400551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/04/2024] [Indexed: 07/06/2024]
Abstract
As information messengers for cell-to-cell communication, exosomes, typically small membrane vesicles (30-150 nm), play an imperative role in the physiological and pathological processes of living systems. Accumulating studies have demonstrated that exosomes are potential biological candidates for theranostics, including liquid biopsy-based diagnosis and drug delivery. However, their clinical applications are hindered by several issues, especially their unspecific detection and insufficient targeting ability. How to upgrade the accuracy of exosome-based theranostics is being widely explored. Aptamers, benefitting from their admirable characteristics, are used as excellent molecular recognition elements to empower exosomes for precision theranostics. With high affinity against targets and easy site-specific modification, aptamers can be incorporated with platforms for the specific detection of exosomes, thus providing opportunities for advancing disease diagnostics. Furthermore, aptamers can be tailored and functionalized on exosomes to enable targeted therapeutics. Herein, this review emphasizes the empowering of exosomes by aptamers for precision theranostics. A brief introduction of exosomes and aptamers is provided, followed by a discussion of recent progress in aptamer-based exosome detection for disease diagnosis, and the emerging applications of aptamer-functionalized exosomes for targeted therapeutics. Finally, current challenges and opportunities in this research field are presented.
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Affiliation(s)
- Liyan Zheng
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/ Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Jin Li
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Yingying Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/ Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Weidi Sun
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/ Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - LeLe Ma
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Fengli Qu
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310024, China
| | - Weihong Tan
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310024, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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4
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de Araújo NS, Moreira ADS, Abreu RDS, Junior VV, Antunes D, Mendonça JB, Sassaro TF, Jurberg AD, Ferreira-Reis R, Bastos NC, Fernandes PV, Guimarães ACR, Degrave WMS, Tilli TM, Waghabi MC. Aptamer-Based Recognition of Breast Tumor Cells: A New Era for Breast Cancer Diagnosis. Int J Mol Sci 2024; 25:840. [PMID: 38255914 PMCID: PMC10815801 DOI: 10.3390/ijms25020840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is one of the leading causes of death among women worldwide and can be classified into four major distinct molecular subtypes based on the expression of specific receptors. Despite significant advances, the lack of biomarkers for detailed diagnosis and prognosis remains a major challenge in the field of oncology. This study aimed to identify short single-stranded oligonucleotides known as aptamers to improve breast cancer diagnosis. The Cell-SELEX technique was used to select aptamers specific to the MDA-MB-231 tumor cell line. After selection, five aptamers demonstrated specific recognition for tumor breast cell lines and no binding to non-tumor breast cells. Validation of aptamer specificity revealed recognition of primary and metastatic tumors of all subtypes. In particular, AptaB4 and AptaB5 showed greater recognition of primary tumors and metastatic tissue, respectively. Finally, a computational biology approach was used to identify potential aptamer targets, which indicated that CSKP could interact with AptaB4. These results suggest that aptamers are promising in breast cancer diagnosis and treatment due to their specificity and selectivity.
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Affiliation(s)
- Natassia Silva de Araújo
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Aline dos Santos Moreira
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Rayane da Silva Abreu
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Valdemir Vargas Junior
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Deborah Antunes
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Julia Badaró Mendonça
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Tayanne Felippe Sassaro
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Arnon Dias Jurberg
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (A.D.J.); (R.F.-R.)
- Laboratório de Animais Transgênicos, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil
- Instituto de Educação Médica (IDOMED), Universidade Estácio de Sá (UNESA)—Campus Vista Carioca, Rio de Janeiro 20071-004, RJ, Brazil
| | - Rafaella Ferreira-Reis
- Laboratório de Pesquisas sobre o Timo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (A.D.J.); (R.F.-R.)
| | - Nina Carrossini Bastos
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil; (N.C.B.); (P.V.F.)
| | - Priscila Valverde Fernandes
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil; (N.C.B.); (P.V.F.)
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
| | - Tatiana Martins Tilli
- Laboratório de Fisiopatologia Clínica e Experimental, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil;
- Plataforma de Oncologia Translacional, Centro de Desenvolvimento Tecnológico em Saúde, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Mariana Caldas Waghabi
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil; (N.S.d.A.); (A.d.S.M.); (R.d.S.A.); (V.V.J.); (D.A.); (J.B.M.); (T.F.S.); (A.C.R.G.); (W.M.S.D.)
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Li D, Su Y, Li J, Liu R, Fang B, He J, Xu W, Zhu L. Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections. Biomacromolecules 2023; 24:4568-4586. [PMID: 37728999 DOI: 10.1021/acs.biomac.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.
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Affiliation(s)
- Diandian Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yuan Su
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Rong Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Bing Fang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jingjing He
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
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Teng X, Wang Y, You L, Wei L, Zhang C, Du Y. Screening a DNA Aptamer Specifically Targeting Integrin β3 and Partially Inhibiting Tumor Cell Migration. Anal Chem 2023; 95:12406-12418. [PMID: 37555842 PMCID: PMC10448441 DOI: 10.1021/acs.analchem.3c01995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
Due to its key roles in malignant tumor progression and reprograming of the tumor microenvironment, integrin β3 has attracted great attention as a new target for tumor therapy. However, the structure-function relationship of integrins β3 remains incompletely understood, leading to the shortage of specific and effective targeting probes. This work uses a purified extracellular domain of integrin β3 and integrin β3-positive cells to screen aptamers, specifically targeting integrin β3 in the native conformation on live cells through the SELEX approach. Following meticulous truncation and characterization of the initial aptamer candidates, the optimized aptamer S10yh2 was produced, exhibiting a low equilibrium dissociation constant (Kd) in the nanomolar range. S10yh2 displays specific recognition of cancer cells with varying levels of integrin β3 expression and demonstrates favorable stability in serum. Subsequent analysis of docking sites revealed that S10yh2 binds to the seven amino acid residues located in the core region of integrin β3. The S10yh2 aptamer can downregulate the level of integrin heterodimer αvβ3 on integrin β3 overexpressed cancer cells and partially inhibit cell migration behavior. In summary, S10yh2 is a promising probe with a small size, simple synthesis, good stability, high binding affinity, and selectivity. It therefore holds great potential for investigating the structure-function relationship of integrins.
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Affiliation(s)
- Xiaoyan Teng
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Yu Wang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liuxia You
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Fujian Medical University, Quanzhou, Fujian 362000, China
| | - Lirong Wei
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
| | - Chao Zhang
- State
Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute,
Department of Oncology, Institute of Molecular Medicine, Renji Hospital,
School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuzhen Du
- Department
of Laboratory Medicine, Shanghai Jiao Tong
University Affiliated Sixth People’s Hospital, Shanghai 200233, China
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7
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Current Status of Oligonucleotide-Based Protein Degraders. Pharmaceutics 2023; 15:pharmaceutics15030765. [PMID: 36986626 PMCID: PMC10055846 DOI: 10.3390/pharmaceutics15030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Transcription factors (TFs) and RNA-binding proteins (RBPs) have long been considered undruggable, mainly because they lack ligand-binding sites and are equipped with flat and narrow protein surfaces. Protein-specific oligonucleotides have been harnessed to target these proteins with some satisfactory preclinical results. The emerging proteolysis-targeting chimera (PROTAC) technology is no exception, utilizing protein-specific oligonucleotides as warheads to target TFs and RBPs. In addition, proteolysis by proteases is another type of protein degradation. In this review article, we discuss the current status of oligonucleotide-based protein degraders that are dependent either on the ubiquitin–proteasome system or a protease, providing a reference for the future development of degraders.
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8
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Sun S, Liu H, Hu Y, Wang Y, Zhao M, Yuan Y, Han Y, Jing Y, Cui J, Ren X, Chen X, Su J. Selection and identification of a novel ssDNA aptamer targeting human skeletal muscle. Bioact Mater 2023; 20:166-178. [PMID: 35663338 PMCID: PMC9157180 DOI: 10.1016/j.bioactmat.2022.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle disorders have posed great threats to health. Selective delivery of drugs and oligonucleotides to skeletal muscle is challenging. Aptamers can improve targeting efficacy. In this study, for the first time, the human skeletal muscle-specific ssDNA aptamers (HSM01, etc.) were selected and identified with Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The HSM01 ssDNA aptamer preferentially interacted with human skeletal muscle cells in vitro. The in vivo study using tree shrews showed that the HSM01 ssDNA aptamer specifically targeted human skeletal muscle cells. Furthermore, the ability of HSM01 ssDNA aptamer to target skeletal muscle cells was not affected by the formation of a disulfide bond with nanoliposomes in vitro or in vivo, suggesting a potential new approach for targeted drug delivery to skeletal muscles via liposomes. Therefore, this newly identified ssDNA aptamer and nanoliposome modification could be used for the treatment of human skeletal muscle diseases.
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Affiliation(s)
- Shuming Sun
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Han Liu
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Yan Hu
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Yanpeng Wang
- Molecular Biology Research Center, Center for Medical Genetics, Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Mingri Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410013, China
| | - Yijun Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Yafei Han
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Yingying Jing
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Jin Cui
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Xiaoxiang Ren
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
| | - Xiao Chen
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Jiacan Su
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- Department of Orthopedics Trauma, Shanghai Changhai Hospital, Naval Medical University, Shanghai, 200433, China
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9
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A review: Construction of aptamer screening methods based on improving the screening rate of key steps. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Liao Y, Xiong S, Ur Rehman Z, He X, Peng H, Liu J, Sun S. The Research Advances of Aptamers in Hematologic Malignancies. Cancers (Basel) 2023; 15:300. [PMID: 36612296 PMCID: PMC9818631 DOI: 10.3390/cancers15010300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Currently, research for hematological malignancies is very intensive, with many breakthroughs. Among them, aptamer-based targeted therapies could be counted. Aptamer is a targeting tool with many unique advantages (easy synthesis, low toxicity, easy modification, low immunogenicity, nano size, long stability, etc.), therefore many experts screened corresponding aptamers in various hematological malignancies for diagnosis and treatment. In this review, we try to summarize and provide the recent progress of aptamer research in the diagnosis and treatment of hematologic malignancies. Until now, 29 aptamer studies were reported in hematologic malignancies, of which 12 aptamers were tested in vivo and the remaining 17 aptamers were only tested in vitro. In this case, 11 aptamers were combined with chemotherapeutic drugs for the treatment of hematologic malignancies, 4 aptamers were used in combination with nanomaterials for the diagnosis and treatment of hematologic malignancies, and some studies used aptamers for the targeted transportation of siRNA and miRNA for targeted therapeutic effects. Their research provides multiple approaches to achieve more targeted goals. These findings show promising and encouraging future for both hematological malignancies basic and clinical trials research.
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Affiliation(s)
| | | | | | | | | | | | - Shuming Sun
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha 410011, China
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11
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Chen Y, Wu X, Li J, Jiang Y, Xu K, Su J. Bone-Targeted Nanoparticle Drug Delivery System: An Emerging Strategy for Bone-Related Disease. Front Pharmacol 2022; 13:909408. [PMID: 35712701 PMCID: PMC9195145 DOI: 10.3389/fphar.2022.909408] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/27/2022] [Indexed: 12/28/2022] Open
Abstract
Targeted delivery by either systemic or local targeting of therapeutics to the bone is an attractive treatment for various bone metabolism diseases such as osteoporosis, osteoarthritis, osteosarcoma, osteomyelitis, etc. To overcome the limitations of direct drug delivery, the combination of bone-targeted agents with nanotechnology has the opportunity to provide a more effective therapeutic approach, where engineered nanoparticles cause the drug to accumulate in the bone, thereby improving efficacy and minimizing side effects. Here, we summarize the current advances in systemic or local bone-targeting approaches and nanosystem applications in bone diseases, which may provide new insights into nanocarrier-delivered drugs for the targeted treatment of bone diseases. We envision that novel drug delivery carriers developed based on nanotechnology will be a potential vehicle for the treatment of currently incurable bone diseases and are expected to be translated into clinical applications.
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Affiliation(s)
- Yulin Chen
- Institute of Translational Medicine, Shanghai University, Shanghai, China.,School of Medicine, Shanghai University, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Xianmin Wu
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai, China
| | - Jiadong Li
- Institute of Translational Medicine, Shanghai University, Shanghai, China.,School of Medicine, Shanghai University, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Yingying Jiang
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Ke Xu
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Jiacan Su
- Institute of Translational Medicine, Shanghai University, Shanghai, China
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12
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Theoretical design and experimental study of new aptamers with the enhanced binding affinity relying on colorimetric assay for tetracycline detection. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Sousa DA, Carneiro M, Ferreira D, Moreira FTC, Sales MGFV, Rodrigues LR. Recent advances in the selection of cancer-specific aptamers for the development of biosensors. Curr Med Chem 2022; 29:5850-5880. [PMID: 35209816 DOI: 10.2174/0929867329666220224155037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
An early diagnosis has the potential to greatly decrease cancer mortality. For that purpose, specific cancer biomarkers have been molecularly targeted by aptamer sequences to enable an accurate and rapid detection. Aptamer-based biosensors for cancer diagnostics are a promising alternative to those using antibodies, due to their high affinity and specificity to the target molecules and advantageous production. Synthetic nucleic acid aptamers are generated by in vitro Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodologies that have been improved over the years to enhance the efficacy and to shorten the selection process. Aptamers have been successfully applied in electrochemical, optical, photoelectrochemical and piezoelectrical-based detection strategies. These aptasensors comprise a sensitive, accurate and inexpensive option for cancer detection being used as point-of-care devices. This review highlights the recent advances in cancer biomarkers, achievements and optimizations made in aptamer selection, as well as the different aptasensors developed for the detection of several cancer biomarkers.
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Affiliation(s)
- Diana A Sousa
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Mariana Carneiro
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Débora Ferreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Felismina T C Moreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Maria Goreti F V Sales
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Lígia R Rodrigues
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
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14
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Zhang H, Jin C, Zhang L, Peng B, Zhang Y, Liu Y, Li L, Ye M, Xiong W, Tan W. CD71-Specific Aptamer Conjugated with Monomethyl Auristatin E for the Treatment of Uveal Melanoma. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32-40. [PMID: 34928139 DOI: 10.1021/acsami.1c13980] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy among adults. Despite significant advances in diagnosis and treatment, the general mortality of UM remains alarmingly high. This calls for the development of new approaches for the treatment of UM, such as targeted cancer therapy. CD71, also known as transferrin receptor 1, is overexpressed in UM cell lines and tissues. Herein, we report the development of a CD71-specific aptamer targeting the XQ-2d-MMAE conjugate that can distinguish UM cells from normal human uveal melanocytes. The cytotoxic drug monomethyl auristatin E (MMAE) could be easily coupled onto XQ-2d, a DNA aptamer that specifically targets CD71, to achieve efficiently targeted cancer growth inhibition in a mouse xenograft model, thus implying that XQ-2d-MMAE might be developed into a promising novel anti-tumor agent for the treatment of UM. Collectively, our results demonstrated that CD71 is a reliable target for drug delivery in UM and could be utilized as a model to explore aptamer-mediated targeted UM treatment strategies.
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Affiliation(s)
- Hui Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, 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
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yibin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Ling Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Wei Xiong
- Department of Ophthalmology, the Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, Hunan 410082, 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
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15
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Pei Y, Wang C, Chen Z, Li S, Chen H, Wang Z, He N. AutoCell Systematic Evolution of Ligands by Exponential Enrichment: The Software Designed and Developed for the Automated Screening System of Nucleic Acid Aptamers. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2021; 21:5363-5369. [PMID: 33875130 DOI: 10.1166/jnn.2021.19342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aptamers are a new kind of nano-probes for bioassays and drug delivery, etc. In this paper, software has been developed as an automatic control center for the automated aptamer selecting system which realized the high integration of aptamer selection, data acquisition and processing. This software, applied in windows system, is developed by C# with the Microsoft Visual Studio 2015 integrated developing environment and the database used in this software is implemented using open source relational database MYSQL. According to the requirement analysis, this software realized various important necessary functions including feasible experiment design, auto-control of the hardware, real time process monitoring and efficient data management which perfectly satisfies the users' demands. During the actual experiment operation, this software worked smoothly and assumed stable serial port communication between it and the hardware, meanwhile, the interaction between the software and MYSQL remained good stability. As a consequence, it is practical and reasonable to apply this software to the automated aptamer selecting system for research.
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Affiliation(s)
- Yuhong Pei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Chao Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhu Chen
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Song Li
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Hui Chen
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Zunliang Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
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16
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Abstract
Multiple myeloma is the second most common hematological malignancy in adults, accounting for 2% of all cancer-related deaths in the UK. Current chemotherapy-based regimes are insufficient, as most patients relapse and develop therapy resistance. This review focuses on current novel antibody- and aptamer-based therapies aiming to overcome current therapy limitations, as well as their respective limitations and areas of improvement. The use of computer modeling methods, as a tool to study and improve ligand-receptor alignments for the use of novel therapy development will also be discussed, as it has become a rapid, reliable and comparatively inexpensive method of investigation.
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17
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Ray RM, Hansen AH, Taskova M, Jandl B, Hansen J, Soemardy C, Morris KV, Astakhova K. Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides. Beilstein J Org Chem 2021; 17:891-907. [PMID: 33981364 PMCID: PMC8093553 DOI: 10.3762/bjoc.17.75] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/09/2021] [Indexed: 01/28/2023] Open
Abstract
Lipid nanoparticles (LNPs) constitute a facile and scalable approach for delivery of payloads to human cells. LNPs are relatively immunologically inert and can be produced in a cost effective and scalable manner. However, targeting and delivery of LNPs across the blood–brain barrier (BBB) has proven challenging. In an effort to target LNPs composed of an ionizable cationic lipid (DLin-MC3-DMA), cholesterol, the phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), and 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000 (DMG-PEG 2000) to particular cell types, as well as to generate LNPs that can cross the BBB, we developed and assessed two approaches. The first was centered on the BBB-penetrating trans-activator of transcription (Tat) peptide or the peptide T7, and the other on RNA aptamers targeted to glycoprotein gp160 from human immunodeficiency virus (HIV) or C-C chemokine receptor type 5 (CCR5), a HIV-1 coreceptor. We report herein a CCR5-selective RNA aptamer that acts to facilitate entry through a simplified BBB model and that drives the uptake of LNPs into CCR5-expressing cells, while the gp160 aptamer did not. We further observed that the addition of cell-penetrating peptides, Tat and T7, did not increase BBB penetration above the aptamer-loaded LNPs alone. Moreover, we found that these targeted LNPs exhibit low immunogenic and low toxic profiles and that targeted LNPs can traverse the BBB to potentially deliver drugs into the target tissue. This approach highlights the usefulness of aptamer-loaded LNPs to increase target cell specificity and potentially deliverability of central-nervous-system-active RNAi therapeutics across the BBB.
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Affiliation(s)
- Roslyn M Ray
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | | | - Maria Taskova
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Bernhard Jandl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Citra Soemardy
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
| | - Kevin V Morris
- Center for Gene Therapy, Beckman Research Institute, City of Hope, Duarte, CA, United States of America.,School of Medical Sciences, Griffith University, Gold Coast, Australia 4222.,Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD 4222, Australia
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
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18
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Duanghathaipornsuk S, Reaver NGF, Cameron BD, Kim DS. Adsorption Kinetics of Glycated Hemoglobin on Aptamer Microarrays with Antifouling Surface Modification. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4647-4657. [PMID: 33797255 DOI: 10.1021/acs.langmuir.1c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Aptamers are oligonucleotides that bind with high affinity to target molecules of interest. One such target is glycated hemoglobin (gHb), a biomarker for assessing glycemic control and diabetes diagnosis. By the coupling of aptamers with surface plasmon resonance (SPR) sensing surfaces, a fast, reliable and inexpensive assay for gHb can be developed. In this study, we tested the affinity of SPR-sensing surfaces, composed of aptamers and antifouling self-assembled monolayers (SAMs), to hemoglobin (Hb) and gHb. First, we developed a gHb-targeted aptamer (GHA) through a modified Systematic Evolution of Ligands by EXponential (SELEX) enrichment process and tested its affinity to gHb using the Nano-Affi protocol. GHA was used to produce three distinct SAM-SPR-sensing surfaces: (Type-1) a SAM of GHA directly attached to a sensor surface; (Type-2) GHA attached to a SAM of 11-mercaptoundecanoic acid (11MUA) on a sensor surface; (Type-3) GHA attached to a binary SAM of 11MUA and 3,6-dioxa-8-mercaptooctan-1-ol (DMOL) on a sensor surface. Type-2 and Type-3 surfaces were characterized by cyclic voltammetry and electrochemical impedance spectroscopy to confirm that GHA bound to the underlying SAMs. The adsorption kinetics for Hb and gHb interacting with each SPR sensing surface were used to quantify their respective affinities. The Type-1 surface without antifouling modification had a dissociation constant ratio (KD,Hb/KD,gHb) of 9.7, as compared to 809.3 for the Type-3 surface, demonstrating a higher association of GHA to gHb for sensor surfaces with antifouling modifications than those without. The enhanced selectivity of GHA to gHb can likely be attributed to the inclusion of DMOL in the SAM-modified surface, which reduced interference from nonspecific adsorption of proteins. Results suggest that pairing aptamers with antifouling SAMs can significantly improve their target affinity, potentially allowing for the development of novel, low cost, and fast assays.
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Affiliation(s)
- Surachet Duanghathaipornsuk
- Department of Chemical Engineering, 2801 W. Bancroft St., University of Toledo, Toledo, Ohio 43606, United States
| | - Nathan G F Reaver
- Engineering School of Sustainable Infrastructure and the Environment Environmental Engineering Sciences, University of Florida, Gainesville, Florida 32611, United States
- Water Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Brent D Cameron
- Department of Bioengineering, 2801 W. Bancroft St., University of Toledo, Toledo, Ohio 43606, United States
| | - Dong-Shik Kim
- Department of Chemical Engineering, 2801 W. Bancroft St., University of Toledo, Toledo, Ohio 43606, United States
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19
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Pu Y, Xiang J, Zhang X, Deng Y, Liu H, Tan W. CD36 as a Molecular Target of Functional DNA Aptamer NAFLD01 Selected against NAFLD Cells. Anal Chem 2021; 93:3951-3958. [PMID: 33596054 DOI: 10.1021/acs.analchem.0c04866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The aim of this study was to identify the target of nonalcoholic fatty liver disease (NAFLD) cell-specific aptamer NAFLD01 and investigate its effect on lipid metabolism in vitro. A distinct membrane protein of NAFLD cells pulled down by NAFLD01 was analyzed by mass spectrometry to determine target candidates, and affinity of NAFLD01 to target-protein-silent NAFLD cells was detected to validate it. Knockdown of CD36 abolished the binding of NAFLD01, and its binding affinity was associated with membrane-bound CD36. NAFLD01 affinity for NAFLD cells was proportional to the CD36 expression level. Moreover, compared to random sequences, NAFLD01 showed better recognition for both mouse and human tissue sections of NAFLD. Importantly, NAFLD01 could ameliorate liver fat deposition through interaction with CD36 in vitro. Therefore, aptamer NAFLD01 could act as an effective and safe targeted drug for NAFLD. NAFLD01 is the first reported CD36-specific aptamer. This aptamer can improve hepatocyte steatosis via specifically binding to CD36. This study provides a molecular tool to investigate the mechanism of CD36 in NAFLD.
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Affiliation(s)
- Ying Pu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Juan Xiang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xinxu Zhang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanyuan Deng
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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20
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Immobilized DNA aptamers used as potent attractors for vascular endothelial cell: in vitro study of female rat. Biosci Rep 2020; 40:221855. [PMID: 31930392 PMCID: PMC6992924 DOI: 10.1042/bsr20182444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 12/23/2019] [Accepted: 12/28/2019] [Indexed: 11/17/2022] Open
Abstract
Vascular endothelial cells are essential to vascular function and maintenance. Dysfunction of these cells can lead to the development of cardiovascular disease or contribute to tumorigenesis. As such, the therapeutic modulation and monitoring of vascular endothelial cells are of significant clinical interest, and several endothelial-specific ligands have been developed for drug delivery and the monitoring of endothelial function. However, the application of these ligands has been limited by their high cost and tendency to induce immune responses, highlighting a need for alternate methods of targeting vascular endothelial cells. In the present study, we explore the therapeutic potential of DNA aptamers. Using cell-SELEX technology, we identified two aptamers with specific binding affinity for vascular endothelial cells and propose that these molecules show potential for use as new ligands for drug and biomarker research concerning vascular endothelial cells.
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21
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Narayan C, Kwon J, Kim C, Kim SJ, Jang SK. Virus-based SELEX (viro-SELEX) allows development of aptamers targeting knotty proteins. Analyst 2020; 145:1473-1482. [PMID: 31868873 DOI: 10.1039/c9an01943j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It has been 100 years since the worst flu (Spanish flu) mankind has ever experienced. Rapid, accurate diagnosis and subtyping of flu are still an urgent unmet medical need. By using surrogate virus-based SELEX (viro-SELEX), we report here multiple advances incorporated into the field of flu diagnostics: (i) aptamers that can bind to the native virus well even though they cannot bind strongly to a recombinant protein (hemagglutinin); (ii) a couple of aptamers that can target a broad range of strains belonging to the H1N1 subtype and detect only the H1N1 subtype and nothing else; (iii) a highly sensitive lateral flow assay system (limit of detection is 0.08 HAU) using fluorescence-tagged aptamers. The viro-SELEX method of aptamer selection in conjunction with a fluorescent tag on aptamers is a very useful approach to develop highly sensitive, specific, portable, rapid, and quantitative point-of-care testing diagnostic tools for the future.
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Affiliation(s)
- Chandan Narayan
- Molecular virology Laboratory, Department of Life Sciences, Postech Biotech Center, Pohang University of Science and Technology, Cheongam-ro 77, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, Republic of Korea.
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22
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Jose J, Thomas AM, Mendonsa D, Al-Sanea MM, Uddin MS, Parambi DGT, Charyulu RN, Mathew B. Aptamers in Drug Design: An Emerging Weapon to Fight a Losing Battle. Curr Drug Targets 2020; 20:1624-1635. [PMID: 31362673 DOI: 10.2174/1389450120666190729121747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/22/2022]
Abstract
Implementation of novel and biocompatible polymers in drug design is an emerging and rapidly growing area of research. Even though we have a large number of polymer materials for various applications, the biocompatibility of these materials remains as a herculean task for researchers. Aptamers provide a vital and efficient solution to this problem. They are usually small (ranging from 20 to 60 nucleotides, single-stranded DNA or RNA oligonucleotides which are capable of binding to molecules possessing high affinity and other properties like specificity. This review focuses on different aspects of Aptamers in drug discovery, starting from its preparation methods and covering the recent scenario reported in the literature regarding their use in drug discovery. We address the limitations of Aptamers and provide valuable insights into their future potential in the areas regarding drug discovery research. Finally, we explained the major role of Aptamers like medical imaging techniques, application as synthetic antibodies, and the most recent application, which is in combination with nanomedicines.
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Affiliation(s)
- Jobin Jose
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Aaron Mathew Thomas
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Darewin Mendonsa
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Mohammad M Al-Sanea
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh.,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Della Grace Thomas Parambi
- College of Pharmacy, Department of Pharmaceutical Chemistry, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - R Narayana Charyulu
- Department of Pharmaceutics, N.G.S.M. Institute of Pharmaceutical Sciences, NITTE Deemed to be University, Mangalore, India
| | - Bijo Mathew
- Division of Drug Design and Medicinal Chemistry Research Lab, Department of Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad 678557, Kerala, India
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23
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Schmitz FRW, Valério A, de Oliveira D, Hotza D. An overview and future prospects on aptamers for food safety. Appl Microbiol Biotechnol 2020; 104:6929-6939. [PMID: 32588103 PMCID: PMC7315907 DOI: 10.1007/s00253-020-10747-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
Abstract
Introduction Many bacteria are responsible for infections in humans and plants, being found in vegetables, water, and medical devices. Most bacterial detection methods are time-consuming and take days to give the result. Aptamers are a promising alternative for a quick and reliable measurement technique to detect bacteria present in food products. Selected aptamers are DNA or RNA oligonucleotides that can bind with bacteria or other molecules with affinity and specificity for the target cells by the SELEX or cell-SELEX technique. This method is based on some rounds to remove the non-ligand oligonucleotides, leaving the aptamers specific to bind to the selected bacteria. Compared with conventional methodologies, the detection approach using aptamers is a rapid, low-cost form of analysis. Objective This review summarizes obtention methods and applications of aptamers in the food industry and biotechnology. Besides, different techniques with aptamers are presented, which enable more effective target detection. Conclusion Applications of aptamers as biosensors, or the association of aptamers with nanomaterials, may be employed in analyses by colorimetric, fluorescence, or electrical devices. Additionally, more efficient ways of sample preparation are presented, which can support food safety to provide human health, with a low-cost method for contaminant detection.Key points • Aptamers are promising for detecting contaminants outbreaks. • Studies are needed to identify aptamers for different targets. |
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Affiliation(s)
- Fernanda Raquel Wust Schmitz
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Alexsandra Valério
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
| | - Débora de Oliveira
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil.
| | - Dachamir Hotza
- Department of Chemical Engineering and Food Engineering (EQA), Federal University of Santa Catarina (UFSC), Florianópolis, SC, 88040-900, Brazil
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Aptamer-navigated copolymeric drug carrier system for in vitro delivery of MgO nanoparticles as insulin resistance reversal drug candidate in Type 2 diabetes. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Zhang N, Zhang ZK, Yu Y, Zhuo Z, Zhang G, Zhang BT. Pros and Cons of Denosumab Treatment for Osteoporosis and Implication for RANKL Aptamer Therapy. Front Cell Dev Biol 2020; 8:325. [PMID: 32478071 PMCID: PMC7240042 DOI: 10.3389/fcell.2020.00325] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
Osteoporosis is age-related deterioration in bone mass and micro-architecture. Denosumab is a novel human monoclonal antibody for osteoporosis. It is a receptor activator of nuclear factor-κB ligand (RANKL) inhibitor, which binds to and inhibits osteoblast-produced RANKL, in turn reduces the binding between RANKL and osteoclast receptor RANK, therefore decreases osteoclast-mediated bone resorption and turnover. However, adverse events have also been reported after denosumab treatment, including skin eczema, flatulence, cellulitis and osteonecrosis of the jaw (ONJ). Extensive researches on the mechanism of adverse reactions caused by denosumab have been conducted and may provide new insights into developing new RANKL inhibitors that achieve better specificity and safety. Aptamers are single-stranded oligonucleotides that can bind to target molecules with high specificity and affinity. They are screened from large single-stranded synthetic oligonucleotides and enriched by a technology named SELEX (systematic evolution of ligands by exponential enrichment). With extra advantages such as high stability, low immunogenicity and easy production over antibodies, aptamers are hypothesized to be promising candidates for therapeutic drugs targeting RANKL to counteract osteoporosis. In this review, we focus on the pros and cons of denosumab treatment in osteoporosis and the implication for novel aptamer treatment.
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Affiliation(s)
- Ning Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Zong-Kang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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26
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ZHAO LP, YANG G, ZHANG XM, QU F. Development of Aptamer Screening against Proteins and Its Applications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60012-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Zhou L, Wang S, Yu Q, Wei S, Liu M, Wei J, Huang Y, Huang X, Li P, Qin Q. Characterization of Novel Aptamers Specifically Directed to Red-Spotted Grouper Nervous Necrosis Virus (RGNNV)-Infected Cells for Mediating Targeted siRNA Delivery. Front Microbiol 2020; 11:660. [PMID: 32425897 PMCID: PMC7203557 DOI: 10.3389/fmicb.2020.00660] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/23/2020] [Indexed: 12/29/2022] Open
Abstract
Nervous necrosis virus (NNV) causes viral nervous necrosis, the most devastating disease in more than 50 fish species worldwide, with massive mortality rates up to 100%, resulting in great economic losses to mariculture. However, few methods are available for the efficient diagnosis and treatment of viral nervous necrosis. Aptamers are molecular recognition ligands characterized by their remarkably high specificity and affinity, great stability, and ease of synthesis, and have been widely studied in application of disease diagnosis and therapies. In this study, we generated three aptamers against red-spotted grouper nervous necrosis virus (RGNNV)-infected grouper brain (GB) cells using the Cell-SELEX (cell based-systematic evolution of ligands by exponential enrichment) technology. The selected aptamers formed stable stem-loop structures, and could specifically recognize RGNNV-infected GB cells, with calculated dissociation constants (Kd) of 27.96, 29.3, and 59.5 nM for aptamers GBN2, GBN10, and GBN34, respectively. They also recognized RGNNV-infected brain tissues. The three aptamers were non-toxic and showed antiviral activities both in vitro and in vivo. Fluorescence microscopy and flow cytometry also demonstrated that aptamer GBN34 could be efficiently and specifically internalized into RGNNV-infected GB cells. The targeted cellular delivery of aptamer-small interfering RNA (siRNA) conjugates remarkably inhibited RGNNV infection in GB cells. The efficiency of the aptamer-based targeted delivery system was about 75% reduction in infection after 48 h, which was similar to that of transfection. These aptamers have great potential utility in the rapid diagnosis and inhibition of RGNNV infection in mariculture.
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Affiliation(s)
- Lingli Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaowen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Qing Yu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Shina Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning, China
| | - Jingguang Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Youhua Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaohong Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Pengfei Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Qiwei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
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Zhong W, Zhang Y, Tan W, Zhang J, Liu J, Wang G, Liao J, Liu B, Chen K, Yu B, Deng Y, Zou Y, Pu Y, Liu H. Adipose specific aptamer adipo-8 recognizes and interacts with APMAP to ameliorates fat deposition in vitro and in vivo. Life Sci 2020; 251:117609. [PMID: 32272180 DOI: 10.1016/j.lfs.2020.117609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
AIMS To identify the target of an adipose specific aptamer adipo-8, predict the potential interaction between adipo-8 and its target, and investigate lipid-lowering effect of adipo-8 in vitro and in vivo. MAIN METHODS Distinct membranous protein of 3T3-L1 adipocyte pulled-down by adipo-8 was mass-spectrometry analyzed as target candidate(s), and affinity of adipo-8 to target protein-silent adipocyte was detected to validate it. Interaction between adipo-8 and target was predicted by bioinformatic analysis, further confirmed by aptamer truncation and competitive binding assay. To investigate lipid-lowering effect of adipo-8 and mechanism behind, 250 nmol/L adipo-8 or library was incubated with 3T3-L1 adipocyte or target-protein-silent adipocyte for 24 h, and 0.01 μg/g/day adipo-8 or library was administrated to high-fat-fed male mice for 21 days. KEY FINDINGS APMAP (Adipocyte Plasma Membrane Associated Protein) was identified as adipo-8 target, and adipo-8 affinity to adipocytes was in proportional to APMAP expression. Docking model between the stem-loop structure of adipo-8 and APMAP were predicted that adipo-8 was likely to interact with APMAP at its amino-acid 275-411 sequence. Moreover, adipo-8 could ameliorate fat deposition through interaction with APMAP in vitro, and administration of adipo-8 in high-fat-diet fed mice resulted in body weight loss and blood triglyceride decrease without liver or renal dysfunction. SIGNIFICANCE Adipo-8 could recognize APMAP specifically and interact with its targets to ameliorate fat deposition in vitro and in vivo. Aptamer adipo-8 has potential to act as an effective and safe targeted drug for obesity and obesity related diseases.
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Affiliation(s)
- Wen Zhong
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yin Zhang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Jiani Zhang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guodong Wang
- Anhui Provincial Engineering Research Center for Polysaccharide Drugs, School of Pharmacy, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Jie Liao
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ke Chen
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuanyuan Deng
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yanbo Zou
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ying Pu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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Xu G, Zhao J, Liu N, Yang M, Zhao Q, Li C, Liu M. Structure-guided post-SELEX optimization of an ochratoxin A aptamer. Nucleic Acids Res 2019; 47:5963-5972. [PMID: 31062016 PMCID: PMC6582339 DOI: 10.1093/nar/gkz336] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/30/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
SELEX is the cornerstone for aptamer research with broad applications in biosensors and medicine. To improve the affinity of selected aptamers, we propose a structure-guided post-SELEX approach, an optimization method based on the precise secondary structure of the aptamer–ligand complex. We demonstrate this approach using the Ochratoxin A (OTA) aptamer. Guided by the structure, we designed a new aptamer whose affinity is improved by more than 50-fold. We also determined the high-resolution NMR structure of the new aptamer-OTA complex and elucidated the discriminatory recognition mechanism of one atomic difference between two analogs, OTA and OTB. The aptamer forms an unusual hairpin structure containing an intramolecular triple helix, which is not seen in the previously determined aptamer complex. The π–π stacking, the hydrophobic interaction, hydrogen bonds and halogen bonds between OTA and the aptamer contribute to the recognition of OTA, and the halogen bonds play an important role in discriminating between OTA and OTB. Our results demonstrate that the structure-guided post-SELEX approach improves aptamers affinity. An improved OTA biosensor system might be developed using this new strategy.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Qiang Zhao
- University of Chinese Academy of Sciences, Beijing 100029, P.R. China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
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30
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Theoretical design and experimental study of new aptamers with the improved target-affinity: New insights into the Pb2+-specific aptamers as a case study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Wu X, Liu H, Han D, Peng B, Zhang H, Zhang L, Li J, Liu J, Cui C, Fang S, Li M, Ye M, Tan W. Elucidation and Structural Modeling of CD71 as a Molecular Target for Cell-Specific Aptamer Binding. J Am Chem Soc 2019; 141:10760-10769. [PMID: 31185171 DOI: 10.1021/jacs.9b03720] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pancreatic cancer is a highly lethal malignancy associated with tissues of the pancreas. Early diagnosis and effective treatment are crucial to improving the survival rate of patients with pancreatic cancer. In a previous study, we employed the cell-SELEX strategy to obtain an ssDNA aptamer termed XQ-2d with high binding affinity for pancreatic cancer. Here, we first identify CD71 as the XQ-2d-binding target. We found that knockdown of CD71 abolished the binding of XQ-2d and that the binding affinity of XQ-2d is associated with membrane-bound CD71, rather than total CD71 levels. Competitive analysis revealed that XQ-2d shares the same binding site on CD71 with transferrin (Tf), but not anti-CD71 antibody. We then used a surface energy transfer (SET) nanoruler to measure the distance between the binding sites of XQ-2d and anti-CD71 antibody, and it was about 15 nm. Furthermore, we did molecular dynamics simulation to clarify that the spatial structure of XQ-2d and Tf competitively binding to CD71. We also engineered XQ-2d-mediated targeted therapy for pancreatic cancer, using an XQ-2d-based complex for loading doxorubicin (Dox). Because CD71 is overexpressed not only in pancreatic cancer but also in a variety of tumors, our work provides a systematic novel way of studying a potential biomarker and also promising tools for cancer diagnosis and therapy, opening new doors for effective cancer theranostics.
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Affiliation(s)
- Xiaoqiu Wu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Honglin Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,School of Food and Biological Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China
| | - Dongmei Han
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Hui Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | | | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , 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, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611 , United States
| | | | | | - Mao Ye
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , 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, McKnight Brain Institute , University of Florida , Gainesville , Florida 32611 , United States.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
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Wu S, Yang N, Zhong L, Luo Y, Wang H, Gong W, Zhou S, Li Y, He J, Cao H, Huang Y, Zhao Y. A novel label-free terbium(iii)-aptamer based aptasensor for ultrasensitive and highly specific detection of acute lymphoma leukemia cells. Analyst 2019; 144:3843-3852. [PMID: 31098604 DOI: 10.1039/c8an02342e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Acute leukemia is a malignant clonal disease of hematopoietic stem cells with a high prevalence and mortality rate. However, there are no efficient tools to facilitate early diagnosis and treatment of leukemia. Therefore, development of new methods for the early diagnosis and prevention of leukemia, especially non-invasive diagnosis at the cellular level, is imperative. Here, a label-free signal-on fluorescence aptasensor based on terbium(iii)-aptamer (Tb3+-apt) was applied for the detection of leukemia. The aptamer sensitizes the fluorescence of Tb3+ and forms the strong fluorescent Tb3+-apt probe. The target cells, the T-cell acute lymphoblastic leukemia cell line (CCRF-CEM) combined with the Tb3+-apt probe to form the Tb3+-apt-CEM complex, were removed by centrifugation, and the supernatant containing a small amount of the Tb3+-apt probe was detected using a fluorescence spectrophotometer. The logarithm of cell concentration showed a good linear relationship (R2 = 0.9881) with the fluorescence signal. The linear range for CCRF-CEM detection was 5-5 × 106 cells per ml, while the detection limit was 5 cells per ml of the binding buffer. Clinical samples were collected from 100 cases, and the specificity and positive rates detected by this method were up to 94% and 90%, respectively. Therefore, a single-stranded DNA-sensitized terbium(iii) luminescence method diagnostic was developed which is rapid, sensitive, and economical and can be used for diagnosis of various types of leukemia at the early stage.
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Affiliation(s)
- Siwen Wu
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Nuo Yang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Liping Zhong
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Yiqun Luo
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Huiling Wang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Wenlin Gong
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Sufang Zhou
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Yanmei Li
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Jian He
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Haopei Cao
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Yong Huang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
| | - Yongxiang Zhao
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
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Wang T, Deng Y, Qu G, Chen Y, Shang J, Feng Z, Zheng J, Yang F, He N. Cell microarray chip system for accurate, rapid diagnosis and target treatment of breast cancer cells SK-BR-3. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wan LY, Yuan WF, Ai WB, Ai YW, Wang JJ, Chu LY, Zhang YQ, Wu JF. An exploration of aptamer internalization mechanisms and their applications in drug delivery. Expert Opin Drug Deliv 2019; 16:207-218. [PMID: 30691313 DOI: 10.1080/17425247.2019.1575808] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION As 'chemical antibodies', aptamers have some advantages, such as lack of immunogenicity, rapid tissue penetration, cell internalization and so on. Consequently, more and more aptamers have been screened out by the systematic evolution of ligands through exponential enrichment for the desired cells or membrane receptors. On the basis of the result, researchers use aptamers to guide drug targeting to the desired cells and internalization in vivo. AREAS COVERED In this review, we explore the mechanisms of cargo- or aptamer-mediated internalization, and then briefly summarize five strategies for exploring the mechanism of aptamer internalization. Finally, we focus on four types of applications involving aptamer internalization: aptamers as drugs, aptamers as chemical drug-delivery systems, aptamer-based chimeras and aptamer-conjugated nanoparticles or block copolymer micelles. EXPERT OPINION Two aptamer-internalization mechanisms are known, namely receptor-mediated endocytosis and macropinocytosis. The latter mechanism, which is has only been verified in the internalization of nucleolin aptamer shuttles between the nucleus and cytoplasm, may be important for nuclear internalization and cargo molecule escape from the endosomal compartment. Thus, it is feasible to use some strategies to further explore the macropinocytosis internalization mechanism and then to screen for aptamers similar to the nucleolin aptamer for use with the desired cell types as a targeted delivery tool.
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Affiliation(s)
- Lin-Yan Wan
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Wen-Fang Yuan
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Wen-Bing Ai
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
| | - Yao-Wei Ai
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Jiao-Jiao Wang
- c Medical College , China Three Gorges University , Yichang , China
| | - Liang-Yin Chu
- e School of Chemical Engineering , Sichuan University , Chengdu , China
| | - Yan-Qiong Zhang
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Jiang-Feng Wu
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
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Liu M, Yang T, Chen Z, Wang Z, He N. Differentiating breast cancer molecular subtypes using a DNA aptamer selected against MCF-7 cells. Biomater Sci 2019; 6:3152-3159. [PMID: 30349922 DOI: 10.1039/c8bm00787j] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides selected by systematic evolution of ligands by exponential enrichment (SELEX), which show great potential in the diagnosis and personalized therapy of cancers, due to their specific advantages over antibodies. In the past years, though great progress has been made in molecular subtyping of breast cancer, it remains a challenge in clinical medicine, which plays a crucial role in the treatment. In this study, a ssDNA aptamer MF3 against MCF-7 breast cancer cells was developed by Cell-SELEX for differentiating breast cancer molecular subtypes, which showed favorable specificity and binding affinity towards MCF-7 cells with a Kd value of 82.25 ± 25.14 nM. The aptamer could not only successfully distinguish MCF-7 breast cancer cells from MDA-MB-231 and SK-BR-3 breast cancer cells and MCF-10A human normal mammary epithelial cells, but also could differentiate MCF-7 cells from other cancer cells or normal cells. Moreover, both in vivo and in vitro fluorescence imaging studies demonstrated that aptamer MF3 was able to distinguish tumor-bearing mice and xenograft tissue sections of MCF-7 breast cancer cells from that of MDA-MB-231 and SK-BR-3 breast cancer cells. All these results suggested that aptamer MF3 is a potential tool for differentiating molecular subtypes and diagnosis of breast cancer.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
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Acquah C, Agyei D, Obeng EM, Pan S, Tan KX, Danquah MK. Aptamers: an emerging class of bioaffinity ligands in bioactive peptide applications. Crit Rev Food Sci Nutr 2019; 60:1195-1206. [PMID: 30714390 DOI: 10.1080/10408398.2018.1564234] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The food and health applications of bioactive peptides have grown remarkably in the past few decades. Current elucidations have shown that bioactive peptides have unique structural arrangement of amino acids, conferring distinct functionalities, and molecular affinity characteristics. However, whereas interest in the biological potency of bioactive peptides has grown, cost-effective techniques for monitoring the structural changes in these peptides and how these changes affect the biological properties have not grown at the same rate. Due to the high binding affinity of aptamers for other biomolecules, they have a huge potential for use in tracking the structural, conformational, and compositional changes in bioactive peptides. This review provides an overview of bioactive peptides and their essential structure-activity relationship. The review further highlights on the types and methods of synthesis of aptamers before the discussion of the prospects, merits, and challenges in the use of aptamers for bioaffinity interactions with bioactive peptides.
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Affiliation(s)
- Caleb Acquah
- Department of Chemical Engineering, Curtin University, Sarawak, Malaysia.,School of Nutrition Sciences, Faculty of Health Sciences, Curtin University, Sarawak, Malaysia
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Eugene Marfo Obeng
- Bioengineering Laboratory, Department of Chemical Engineering, Monash University, Victoria, Australia
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kei Xian Tan
- Department of Chemical Engineering, Curtin University, Sarawak, Malaysia
| | - Michael Kobina Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee, USA
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Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie 2018; 154:132-155. [PMID: 30193856 DOI: 10.1016/j.biochi.2018.09.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method used to isolate high-affinity single stranded oligonucleotides from a large random sequence pool. These SELEX-derived oligonucleotides named aptamer, can be selected against a broad spectrum of target molecules including proteins, cells, microorganisms and chemical compounds. Like antibodies, aptamers have a great potential in interacting with and binding to their targets through structural recognition and are therefore called "chemical antibodies". However, aptamers offer advantages over antibodies including smaller size, better tissue penetration, higher thermal stability, lower immunogenicity, easier production, lower cost of synthesis and facilitated conjugation or modification with different functional moieties. Thus, aptamers represent an attractive substitution for protein antibodies in the fields of biomarker discovery, diagnosis, imaging and targeted therapy. Enormous interest in aptamer technology triggered the development of SELEX that has underwent numerous modifications since its introduction in 1990. This review will discuss the recent advances in SELEX methods and their advantages and limitations. Aptamer applications are also briefly outlined in this review.
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Affiliation(s)
- Payam Bayat
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Khedri
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Zhang H, Wang Z, Xie L, Zhang Y, Deng T, Li J, Liu J, Xiong W, Zhang L, Zhang L, Peng B, He L, Ye M, Hu X, Tan W. Molecular Recognition and In-Vitro-Targeted Inhibition of Renal Cell Carcinoma Using a DNA Aptamer. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:758-768. [PMID: 30141409 PMCID: PMC6108068 DOI: 10.1016/j.omtn.2018.07.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 01/12/2023]
Abstract
Renal cell carcinoma (RCC) is the most common malignant tumor of the urinary system, and it has a high frequency of local invasion and distant metastasis. Although multiple advances have been made in the diagnosis and therapy of RCC, the vast majority of patients with metastatic RCC remain incurable. In this study, an aptamer named SW-4 against RCC 786-O cells was identified from a known sequence pool. The identified aptamer exhibited high binding affinity for target cells with dissociation constants in the nanomolar range. Binding analysis revealed that SW-4 only bound to RCC 786-O cells, but not HEK293T cells or human proximal tubular HK-2 cells, indicating that SW-4 has excellent binding selectivity. By sequence optimization, the 26-nt truncated SW-4b demonstrated improved binding affinity, and it was internalized into target cells via caveolae-mediated endocytosis in a temperature-dependent manner. Furthermore, fluorescence imaging confirmed that SW-4b accumulated at tumor sites in 786-O xenograft nude mice models and specifically recognized clinical RCC tissues. Meanwhile, SW-4b inhibited proliferation of 786-O cells by arresting cell cycle progression at the S phase. Taken together, these results indicate that SW-4b is a potential candidate for development into a novel tool for diagnosis and targeted therapy of RCC.
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Affiliation(s)
- Hui Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Zhibo Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Lin Xie
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Yibin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Tanggang Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Jing Liu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wei Xiong
- Ophthalmology and Eye Research Center, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Lei Zhang
- Department of Nephrology, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Lin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Bo Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Leye He
- Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China.
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Li WM, Zhou LL, Zheng M, Fang J. Selection of Metastatic Breast Cancer Cell-Specific Aptamers for the Capture of CTCs with a Metastatic Phenotype by Cell-SELEX. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:707-717. [PMID: 30098503 PMCID: PMC6083002 DOI: 10.1016/j.omtn.2018.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022]
Abstract
Circulating tumor cells (CTCs) have the potential to predict metastasis, and the capture of CTCs based on their surface markers is mostly applied for CTC detection. Considering that the CTCs with a metastatic phenotype preferably form a metastatic focus and that aptamers have the ability to bind targets with high specificity and affinity, we selected aptamers directed toward metastatic cells by subtractive Cell-SELEX technology using highly metastatic MDA-MB-231 cells as the target cell and low-metastatic MCF-7 cells as the negative cell for the capture of metastatic CTCs. Affinity and selectivity assays showed that aptamer M3 had the highest affinity, with a KD of 45.6 ± 1.2 nM, and had good specificity against several other types of metastatic cancer cells. Based on these findings, we developed an M3-based capture system for CTC enrichment, which has the capability to specifically capture the metastatic cells MDA-MB-231 mixed with non-metastatic MCF-7 cells and CTCs derived from the peripheral blood from metastatic breast cancer patients. A further comparative analysis with the anti-EpCAM probe showed that M3 probe captured epithelial feature-deletion metastatic cells. We developed an aptamer-based CTC capture system through the selection of aptamers by taking whole metastatic cells, not known molecules, as targets, which provided a new insight into CTC capture and Cell-SELEX application.
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Affiliation(s)
- Wan-Ming Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Lin-Lin Zhou
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China; Institute of Immunotherapy, Fujian Medical University, Fuzhou 350122, China
| | - Min Zheng
- Department of Chemotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Jin Fang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China.
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Hoyos-Nogués M, Gil FJ, Mas-Moruno C. Antimicrobial Peptides: Powerful Biorecognition Elements to Detect Bacteria in Biosensing Technologies. Molecules 2018; 23:molecules23071683. [PMID: 29996565 PMCID: PMC6100210 DOI: 10.3390/molecules23071683] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 11/25/2022] Open
Abstract
Bacterial infections represent a serious threat in modern medicine. In particular, biofilm treatment in clinical settings is challenging, as biofilms are very resistant to conventional antibiotic therapy and may spread infecting other tissues. To address this problem, biosensing technologies are emerging as a powerful solution to detect and identify bacterial pathogens at the very early stages of the infection, thus allowing rapid and effective treatments before biofilms are formed. Biosensors typically consist of two main parts, a biorecognition moiety that interacts with the target (i.e., bacteria) and a platform that transduces such interaction into a measurable signal. This review will focus on the development of impedimetric biosensors using antimicrobial peptides (AMPs) as biorecognition elements. AMPs belong to the innate immune system of living organisms and are very effective in interacting with bacterial membranes. They offer unique advantages compared to other classical bioreceptor molecules such as enzymes or antibodies. Moreover, impedance-based sensors allow the development of label-free, rapid, sensitive, specific and cost-effective sensing platforms. In summary, AMPs and impedimetric transducers combine excellent properties to produce robust biosensors for the early detection of bacterial infections.
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Affiliation(s)
- Mireia Hoyos-Nogués
- Biomaterials, Biomechanics and Tissue Engineering Group (BBT), Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain.
- Barcelona Research Center in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain.
| | - F J Gil
- Biomaterials, Biomechanics and Tissue Engineering Group (BBT), Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain.
- Universitat Internacional de Catalunya (UIC), 08195 Sant Cugat del Vallès, Spain.
| | - Carlos Mas-Moruno
- Biomaterials, Biomechanics and Tissue Engineering Group (BBT), Department of Materials Science and Metallurgical Engineering, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain.
- Barcelona Research Center in Multiscale Science and Engineering, UPC, 08019 Barcelona, Spain.
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Duan M, Long Y, Yang C, Wu X, Sun Y, Li J, Hu X, Lin W, Han D, Zhao Y, Liu J, Ye M, Tan W. Selection and characterization of DNA aptamer for metastatic prostate cancer recognition and tissue imaging. Oncotarget 2017; 7:36436-36446. [PMID: 27183906 PMCID: PMC5095011 DOI: 10.18632/oncotarget.9262] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/02/2016] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PCa) is the second leading cause of death and most prevalent cancer in men. The absence of curative options for castration-resistant metastatic prostate cancer and biomarkers able to discriminate between indolent and aggressive tumors contribute to these statistics. In this study, a DNA aptamer termed DML-7 was successfully selected against human PCa cell line DU145 by using the cell-based systematic evolution of ligands by exponential enrichment (SELEX) method. The selected aptamer DML-7 was found to internalize into target cells in a temperature-dependent manner and exhibit high binding affinity for target cells with dissociation constants in the nanomolar range. Binding analysis further revealed that DML-7 only binds to DU145 and PC-3 cells with metastatic potential, but not to LNCaP or 22Rv1 cells with low or nonmetastatic potential, demonstrating that DML-7 has excellent selectivity for the recognition of the metastatic PCa cells. Clinical tissue imaging further confirmed these results. Therefore, both high binding affinity and specificity to metastatic PCa cells and tissues afford DML-7 with the potential for development into a novel tool for diagnosis and targeted drug delivery against metastatic prostate cancer.
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Affiliation(s)
- Minlan Duan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yuqian Long
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoqiu Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yang Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Wei Lin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Dongmei Han
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Jing Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China.,Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, University Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:199-214. [PMID: 29499933 PMCID: PMC5862129 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
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Graphene-based label-free electrochemical aptasensor for rapid and sensitive detection of foodborne pathogen. Anal Bioanal Chem 2017; 409:6893-6905. [PMID: 29030671 DOI: 10.1007/s00216-017-0654-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/11/2017] [Accepted: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Reduced graphene oxide (rGO) has emerged as a promising nanomaterial for reliable detection of pathogenic bacteria due to its exceptional properties such as ultrahigh electron transfer ability, large surface to volume ratio, biocompatibility, and its unique interactions with DNA bases of the aptamer. In this study, rGO-azophloxine (AP) nanocomposite aptasensor was developed for a sensitive, rapid, and robust detection of foodborne pathogens. Besides providing an excellent conductive and soluble rGO nanocomposite, the AP dye also acts as an electroactive indicator for redox reactions. The interaction of the label-free single-stranded deoxyribonucleic acid (ssDNA) aptamer with the test organism, Salmonella enterica serovar Typhimurium (S. Typhimurium), was monitored by differential pulse voltammetry analysis, and this aptasensor showed high sensitivity and selectivity for whole-cell bacteria detection. Under optimum conditions, this aptasensor exhibited a linear range of detection from 108 to 101 cfu mL-1 with good linearity (R 2 = 0.98) and a detection limit of 101 cfu mL-1. Furthermore, the developed aptasensor was evaluated with non-Salmonella bacteria and artificially spiked chicken food sample with S. Typhimurium. The results demonstrated that the rGO-AP aptasensor possesses high potential to be adapted for the effective and rapid detection of a specific foodborne pathogen by an electrochemical approach. Graphical abstract Fabrication of graphene-based nanocomposite aptasensor for detection of foodborne pathogen.
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Soundy J, Day D. Selection of DNA aptamers specific for live Pseudomonas aeruginosa. PLoS One 2017; 12:e0185385. [PMID: 28937998 PMCID: PMC5609762 DOI: 10.1371/journal.pone.0185385] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/12/2017] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes significant morbidity and mortality in immunocompromised patients, particular cystic fibrosis sufferers, burns victims, diabetics and neonates. It thrives in moist places where it forms biofilms that are exceedingly difficult to eradicate on hospital surfaces, in water supplies and implanted biomaterials. Using a live cell SELEX approach we selected DNA aptamers to P. aeruginosa grown as biofilms in microfluidic cells. From a pool of aptamer candidates showing tight binding a stem-loop structure was identified as being important for binding. Enhanced binding and increased specificity was achieved by truncating structures and generating chimeric aptamers from the pool of top candidates. The top candidates have low nanomolar binding constants and high discrimination for P. aeruginosa over other Gram-negative bacteria. The aptamers bind both planktonic grown and biofilm grown cells. They do not have intrinsic bacteriostatic or bactericidal activity, but are ideal candidates for modification for use as aptamer-drug conjugates and in biosensors.
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Affiliation(s)
- Jennifer Soundy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Darren Day
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- * E-mail:
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Ranches G, Lukasser M, Schramek H, Ploner A, Stasyk T, Mayer G, Mayer G, Hüttenhofer A. In Vitro Selection of Cell-Internalizing DNA Aptamers in a Model System of Inflammatory Kidney Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:198-210. [PMID: 28918021 PMCID: PMC5504087 DOI: 10.1016/j.omtn.2017.06.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 12/29/2022]
Abstract
Chronic kidney disease (CKD) is a progressive pathological condition marked by a gradual loss of kidney function. Treatment of CKD is most effective when diagnosed at an early stage and patients are still asymptomatic. However, current diagnostic biomarkers (e.g., serum creatinine and urine albumin) are insufficient for prediction of the pathogenesis of the disease. To address this need, we applied a cell-SELEX (systematic evolution of ligands by exponential enrichment) approach and identified a series of DNA aptamers, which exhibit high affinity and selectivity for cytokine-stimulated cells, resembling some aspects of a CKD phenotype. The cell-SELEX approach was driven toward the enrichment of aptamers that internalize via the endosomal pathway by isolating the endosomal fractions in each selection cycle. Indeed, we demonstrated co-localization of selected aptamers with lysosomal-associated membrane protein 1 (LAMP-1), a late endosomal and lysosomal marker protein, by fluorescence in situ hybridization. These findings are consistent with binding and subsequent internalization of the aptamers into cytokine-stimulated cells. Thus, our study sets the stage for applying selected DNA aptamers as theragnostic reagents for the development of targeted therapies to combat CKD.
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Affiliation(s)
- Glory Ranches
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria; Division of Medical Biochemistry, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Melanie Lukasser
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Herbert Schramek
- Division of Nephrology and Hypertension, Department of Internal Medicine IV, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Andreas Ploner
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria; Sandoz GmbH, Biochemiestrasse 10, Kundl 6250, Austria
| | - Taras Stasyk
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Gert Mayer
- Division of Nephrology and Hypertension, Department of Internal Medicine IV, Medical University Innsbruck, Innsbruck 6020, Austria.
| | - Günter Mayer
- Life and Medical Sciences Institute, Chemical Biology and Chemical Genetics, University of Bonn, Bonn 53115, Germany; Centre of Aptamer Research and Development, University of Bonn, Bonn 53115, Germany
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innsbruck 6020, Austria.
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Batool S, Bhandari S, George S, Okeoma P, Van N, Zümrüt HE, Mallikaratchy P. Engineered Aptamers to Probe Molecular Interactions on the Cell Surface. Biomedicines 2017; 5:biomedicines5030054. [PMID: 28850067 PMCID: PMC5618312 DOI: 10.3390/biomedicines5030054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/01/2017] [Accepted: 08/08/2017] [Indexed: 01/08/2023] Open
Abstract
Significant progress has been made in understanding the nature of molecular interactions on the cell membrane. To decipher such interactions, molecular scaffolds can be engineered as a tool to modulate these events as they occur on the cell membrane. To guarantee reliability, scaffolds that function as modulators of cell membrane events must be coupled to a targeting moiety with superior chemical versatility. In this regard, nucleic acid aptamers are a suitable class of targeting moieties. Aptamers are inherently chemical in nature, allowing extensive site-specific chemical modification to engineer sensing molecules. Aptamers can be easily selected using a simple laboratory-based in vitro evolution method enabling the design and development of aptamer-based functional molecular scaffolds against wide range of cell surface molecules. This article reviews the application of aptamers as monitors and modulators of molecular interactions on the mammalian cell surface with the aim of increasing our understanding of cell-surface receptor response to external stimuli. The information gained from these types of studies could eventually prove useful in engineering improved medical diagnostics and therapeutics.
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Affiliation(s)
- Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Sanam Bhandari
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Shanell George
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Precious Okeoma
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Nabeela Van
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
| | - Hazan E Zümrüt
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd. West, Bronx, New York, NY 10468, USA.
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.
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Meirinho SG, Dias LG, Peres AM, Rodrigues LR. Electrochemical aptasensor for human osteopontin detection using a DNA aptamer selected by SELEX. Anal Chim Acta 2017; 987:25-37. [PMID: 28916037 DOI: 10.1016/j.aca.2017.07.071] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/30/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
Abstract
A DNA aptamer with affinity and specificity for human osteopontin (OPN), a potential breast cancer biomarker, was selected using the SELEX process, considering its homology rate and the stability of its secondary structures. This aptamer exhibited a satisfactory affinity towards OPN, showing dissociation constants lower than 2.5 nM. It was further used to develop a simple, label-free electrochemical aptasensor against OPN. The aptasensor showed good sensitivity towards OPN in standard solutions, being the square wave voltammetry (SWV), compared to the cyclic voltammetry, the most sensitive technique with detection and quantification limits of 1.4 ± 0.4 nM and 4.2 ± 1.1 nM, respectively. It showed good reproducibility and acceptable selectivity, exhibiting low signal interferences from other proteins, as thrombin, with 2.6-10 times lower current signals-off than for OPN. The aptasensor also successfully detected OPN in spiked synthetic human plasma. Using SWV, detection and quantification limits (1.3 ± 0.1 and 3.9 ± 0.4 nM) within the OPN plasma levels reported for patients with breast cancer (0.4-4.5 nM) or with metastatic or recurrent breast cancer (0.9-8.4 nM) were found. Moreover, preliminary assays, using a sample of human plasma, showed that the aptasensor and the standard ELISA method quantified similar OPN levels (2.2 ± 0.7 and 1.7 ± 0.1 nM, respectively). Thus, our aptasensor coupled with SWV represents a promising alternative for the detection of relevant breast cancer biomarkers.
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Affiliation(s)
- Sofia G Meirinho
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luís G Dias
- ESA - Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal; CQ-VR - Centro de Química - Vila Real, University of Trás-os-Montes, Apartado 1013, 5001-801 Vila Real, Portugal
| | - António M Peres
- Laboratory of Separation and Reaction Engineering, Laboratory of Catalysis and Materials (LSRE-LCM), ESA, Instituto Politécnico de Bragança, Campus Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Tan KX, Danquah MK, Sidhu A, Lau SY, Ongkudon CM. Biophysical characterization of layer-by-layer synthesis of aptamer-drug microparticles for enhanced cell targeting. Biotechnol Prog 2017; 34:249-261. [PMID: 28699244 DOI: 10.1002/btpr.2524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 05/04/2017] [Indexed: 11/12/2022]
Abstract
Targeted delivery of drug molecules to specific cells in mammalian systems demonstrates a great potential to enhance the efficacy of current pharmaceutical therapies. Conventional strategies for pharmaceutical delivery are often associated with poor therapeutic indices and high systemic cytotoxicity, and this result in poor disease suppression, low surviving rates, and potential contraindication of drug formulation. The emergence of aptamers has elicited new research interests into enhanced targeted drug delivery due to their unique characteristics as targeting elements. Aptamers can be engineered to bind to their cognate cellular targets with high affinity and specificity, and this is important to navigate active drug molecules and deliver sufficient dosage to targeted malignant cells. However, the targeting performance of aptamers can be impacted by several factors including endonuclease-mediated degradation, rapid renal filtration, biochemical complexation, and cell membrane electrostatic repulsion. This has subsequently led to the development of smart aptamer-immobilized biopolymer systems as delivery vehicles for controlled and sustained drug release to specific cells at effective therapeutic dosage and minimal systemic cytotoxicity. This article reports the synthesis and in vitro characterization of a novel multi-layer co-polymeric targeted drug delivery system based on drug-loaded PLGA-Aptamer-PEI (DPAP) formulation with a stage-wise delivery mechanism. A thrombin-specific DNA aptamer was used to develop the DPAP system while Bovine Serum Albumin (BSA) was used as a biopharmaceutical drug in the synthesis process by ultrasonication. Biophysical characterization of the DPAP system showed a spherical shaped particulate formulation with a unimodal particle size distribution of average size ∼0.685 µm and a zeta potential of +0.82 mV. The DPAP formulation showed a high encapsulation efficiency of 89.4 ± 3.6%, a loading capacity of 17.89 ± 0.72 mg BSA protein/100 mg PLGA polymeric particles, low cytotoxicity and a controlled drug release characteristics in 43 days. The results demonstrate a great promise in the development of DPAP formulation for enhanced in vivo cell targeting. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:249-261, 2018.
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Affiliation(s)
- Kei X Tan
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Michael K Danquah
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Amandeep Sidhu
- Curtin Sarawak Research Institute, Curtin University, Sarawak, 98009, Malaysia.,Faculty of Health Sciences, Curtin University, Perth, 6102, Australia
| | - Sie Yon Lau
- Dept. of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
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Maio G, Enweronye O, Zumrut HE, Batool S, Van N, Mallikaratchy P. Systematic optimization and modification of a DNA aptamer with 2'-O-methyl RNA analogues. ChemistrySelect 2017; 2:2335-2340. [PMID: 29226219 DOI: 10.1002/slct.201700359] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Nucleic acid aptamers (NAAs) are short synthetic DNA or RNA molecules that specifically fold into distinct three-dimensional structures able to specifically recognize a target. While NAAs show unprecedented promise in a variety of applications, including sensing, therapeutics and diagnostics, one major limitation involves the lack of stability towards omnipresent nucleases. Therefore, we herein report a systematic truncation and incorporation of 2'-O-methyl bases to a DNA aptamer, which results in increased stability without affecting affinity. One of the newly designed analogues is stable up to 24 hours, demonstrating that 2'-O-methyl RNA is an attractive modification to DNA aptamers, especially when therapeutic applications are intended.
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Affiliation(s)
- George Maio
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Osita Enweronye
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Hasan E Zumrut
- Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sana Batool
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Nabeela Van
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468.,Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.,Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
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50
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Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach. Sci Rep 2017; 7:42741. [PMID: 28218293 PMCID: PMC5316983 DOI: 10.1038/srep42741] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/12/2017] [Indexed: 02/07/2023] Open
Abstract
Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood. To develop ADAPT, we enriched a library of ~1011 ssODNs for those associating with exosomes from breast cancer patients or controls. The resulting 106 enriched ssODNs were then profiled against plasma from independent groups of healthy and breast cancer-positive women. ssODN-mediated affinity purification and mass spectrometry identified low-abundance exosome-associated proteins and protein complexes, some with known significance in both normal homeostasis and disease. Sequencing of the recovered ssODNs provided quantitative measures that were used to build highly accurate multi-analyte signatures for patient classification. Probing plasma from 500 subjects with a smaller subset of 2000 resynthesized ssODNs stratified healthy, breast biopsy-negative, and -positive women. An AUC of 0.73 was obtained when comparing healthy donors with biopsy-positive patients.
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