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Rezaee MA, Shobeiri SS, Moghadam M, Mashayekhi K, Sankian M. In vitro identification of single-stranded DNA aptamers targeting human IL-23 using the protein-SELEX strategy. J Pharm Biomed Anal 2024; 247:116245. [PMID: 38810331 DOI: 10.1016/j.jpba.2024.116245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/15/2024] [Accepted: 05/19/2024] [Indexed: 05/31/2024]
Abstract
Interleukin (IL)-23 inhibitor monoclonal antibodies shown significant efficacy in treating autoimmune diseases. DNA or RNA aptamers exhibit comparable specificity to antibodies, are cost-effective, non-immunogenic, and do not have batch to batch variation. This study aimed to characterize a single-stranded DNA (ssDNA) aptamer targeting human IL-23. The alpha subunit of IL-23 (P19) and intact IL-23 were cloned, expressed, and the proteins finally were purified through Ni2+-iminodiacetic acid affinity chromatography. The selection and characterization of ssDNA aptamer against P19 were conducted using the protein-systematic evolution of ligands by exponential enrichment (SELEX). Dot blot assay was carried out to monitor binding of the aptamer output of SELEX rounds, to P19 protein. The dissociation constant (Kd) of aptamers with positive results in dot blot assay, determined based on their binding to IL-23 using an ELISA method. Recombinant P19 and IL-23 proteins were 26 and 72 kDa, respectively, observed on SDS-PAGE .12 %. The aptamers output from 7, 8, 9, 10, 11, and 12 rounds of the SELEX was monitored by dot blot assay, revealing that the aptamer from the round 8 has stronger luminescent signal and was selected for TA-cloning. After analyzing the biotinylated aptamers from clones, positive clones in dot blot assay and ELISA were sequenced. Finally, the Kd calculation revealed three aptamers with high affinity, named A23P3, A23P6, and A23P15 with Kd values of 1.37, 2.139, and 2.88 nM, respectively. Results of this study introduced three specific anti-IL-23 ssDNA aptamers with high affinity, which could be utilized for therapeutic and diagnostic purposes.
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Affiliation(s)
- Mohammad Ali Rezaee
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Laboratory Sciences, Faculty of Paramedical, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Saeideh Sadat Shobeiri
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Malihe Moghadam
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kazem Mashayekhi
- Department of Immunology, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mojtaba Sankian
- Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Al Borhani W, Chrouda A, Eissa S, Zourob M. Selection of a new aptamer targeting amoxicillin for utilization in a label-free electrochemical biosensor. Talanta 2024; 276:126245. [PMID: 38788377 DOI: 10.1016/j.talanta.2024.126245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Pharmaceutical pollution has received considerable attention because of the harmful effects of pharmaceutical compounds on human health, even in trace amounts. Amoxicillin is one of the frequently used antibiotics that was included in the list of emerging water pollutants. Therefore, a highly selective and rapid technique for amoxicillin detection is required. In this work, a new aptamer was selected for amoxicillin and utilized for the development of a label-free electrochemical aptasensor. Aptamer selection was performed using the systematic evolution of ligands by exponential enrichment. The selected aptamer showed good specificity against other antibiotics, including the structurally related antibiotics: ampicillin and ciprofloxacin. Among the selected aptamers, Amx3 exhibited the lowest dissociation constant value of 112.9 nM. An aptasensor was developed by immobilization of thiolated Amx3 aptamer onto gold screen-printed electrodes via self-assembly, which was characterized using cyclic voltammetry and electrochemical impedance spectroscopy. The detection was realized by monitoring the change in the differential pulse voltammetry peak current in the ferro/ferricyanide redox couple upon binding of the aptasensor to amoxicillin. The aptasensor showed very good sensitivity with an ultralow limit of detection of 0.097 nM. When the aptasensor was tested using actual spiked milk samples, excellent recovery percentages were observed. The label-free electrochemical aptasensor developed herein is a promising tool for the selective and sensitive detection of amoxicillin in environmental samples.
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Affiliation(s)
- Wafaa Al Borhani
- Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Amani Chrouda
- Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Shimaa Eissa
- Department of Chemistry, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates; Center for Catalysis and Separations, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates.
| | - Mohammed Zourob
- Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia.
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Campos-Fernández E, Alqualo NO, Vaz ER, Rodrigues CM, Alonso-Goulart V. Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice. Biophys Chem 2024; 311:107259. [PMID: 38763045 DOI: 10.1016/j.bpc.2024.107259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
The DNA and RNA aptamers D4 and R4, respectively, emerged from the modification of PC-3 cell-binding aptamer A4. Our objective was to characterize the aptamers in silico and in vitro and begin to identify their target molecules. We represented their structures using computational algorithms; evaluated their binding to several prostate cell lines and their effects on the viability and migration of these cells; and determined their dissociation constant by flow cytometry. We analyzed circulating prostate tumor cells from patients using D4, R4, anti-CD133 and anti-CD44. Finally, the target proteins of both aptamers were precipitated and identified by mass spectrometry to simulate their in silico docking. The aptamers presented similar structures and bound to prostate tumor cells without modifying the cellular parameters studied, but with different affinities. The ligand cells for both aptamers were CD44+, indicating that they could identify cells in the mesenchymal stage of the metastatic process. The possible target proteins NXPE1, ADAM30, and MUC6 need to be further studied to better understand their interaction with the aptamers. These results support the development of new assays to determine the clinical applications of D4 and R4 aptamers in prostate cancer.
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Affiliation(s)
- Esther Campos-Fernández
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Nathalia Oliveira Alqualo
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Emília Rezende Vaz
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Cláudia Mendonça Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Vivian Alonso-Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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4
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Fang Z, Feng X, Tang F, Jiang H, Han S, Tao R, Lu C. Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach. BIOSENSORS 2024; 14:350. [PMID: 39056626 PMCID: PMC11274700 DOI: 10.3390/bios14070350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.
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Affiliation(s)
- Zhihui Fang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Xiaorui Feng
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Fan Tang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Han Jiang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Shuyuan Han
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
| | - Ran Tao
- Shenzhen Key Laboratory of Advanced Thin Films and Applications, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (Z.F.); (X.F.); (F.T.); (H.J.); (S.H.)
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5
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Liao X, Huang L, Pu C, Li S, Feng B, Bai Y. The non-negligible non-specific adsorption of oligonucleotides in target-immobilized Mag-SELEX. Int J Biol Macromol 2024; 275:133649. [PMID: 38972649 DOI: 10.1016/j.ijbiomac.2024.133649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/09/2024]
Abstract
Target-immobilized magnetic beads-based Systematic Evolution of Ligands by Exponential Enrichment (target-immobilized Mag-SELEX) has emerged as a powerful tool for aptamer selection owing to its convenience, efficiency, and versatility. However, in this study we systematically investigated non-specific adsorption in target-immobilized Mag-SELEX and found that the non-specific adsorption of the oligonucleotides to target-labeled magnetic beads was comparable to that of the screening libraries, indicating a substantial portion of captured sequences likely stem from non-specific adsorption. Longer nucleic acid sequences (80 nt and above, such as polyA80 and yeast tRNA) were found to attenuate this non-specific adsorption, with more complex higher-order structures demonstrating greater efficacy, while dNTP and short sequences such as primer sequences (20 nt), polyT(59), or polyA(59), did not possess this capability. Various evidence suggested that hydrophobic interactions and other weak interactions may be the primary underlying cause of non-specific adsorption. Additionally, surface modification of magnetic beads with polar molecule polyethylene glycol (PEG) also yielded a significant reduction in non-specific adsorption. In conclusion, our research underscores the critical importance of closely monitoring non-specific adsorption in target-immobilized Mag-SELEX.
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Affiliation(s)
- Xiaoyan Liao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Guangzhou Huali Science and Technology Vocational College, Guangzhou 511325, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Liujuan Huang
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Chunmin Pu
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Song Li
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Bo Feng
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yalong Bai
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
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Ram TB, Krishnan S, Jeevanandam J, Danquah MK, Thomas S. Emerging Biohybrids of Aptamer-Based Nano-Biosensing Technologies for Effective Early Cancer Detection. Mol Diagn Ther 2024; 28:425-453. [PMID: 38775897 DOI: 10.1007/s40291-024-00717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/28/2024]
Abstract
Cancer is a leading global cause of mortality, which underscores the imperative of early detection for improved patient outcomes. Biorecognition molecules, especially aptamers, have emerged as highly effective tools for early and accurate cancer cell identification. Aptamers, with superior versatility in synthesis and modification, offer enhanced binding specificity and stability compared with conventional antibodies. Hence, this article reviews diagnostic strategies employing aptamer-based biohybrid nano-biosensing technologies, focusing on their utility in detecting cancer biomarkers and abnormal cells. Recent developments include the synthesis of nano-aptamers using diverse nanomaterials, such as metallic nanoparticles, metal oxide nanoparticles, carbon-derived substances, and biohybrid nanostructures. The integration of these nanomaterials with aptamers significantly enhances sensitivity and specificity, promising innovative and efficient approaches for cancer diagnosis. This convergence of nanotechnology with aptamer research holds the potential to revolutionize cancer treatment through rapid, accurate, and non-invasive diagnostic methods.
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Affiliation(s)
| | | | - Jaison Jeevanandam
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Madeira, Portugal.
| | - Michael K Danquah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Sabu Thomas
- School of Polymer Science and Technology and School of Chemical Sciences, Mahatma Gandhi University, Kottayam, Kerala, India
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Wang Z, Che S, Yu Z. PROTAC: Novel degradable approach for different targets to treat breast cancer. Eur J Pharm Sci 2024; 198:106793. [PMID: 38740076 DOI: 10.1016/j.ejps.2024.106793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
The revolutionary Proteolysis Targeting Chimera (PROTACs) have the exciting potential to reshape the pharmaceutical industry landscape by leveraging the ubiquitin-proteasome system for targeted protein degradation. Breast cancer, the most prevalent cancer in women, could be treated using PROTAC therapy. Although substantial work has been conducted, there is not yet a comprehensive overview or progress update on PROTAC therapy for breast cancer. Hence, in this article, we've compiled recent research progress focusing on different breast cancer target proteins, such as estrogen receptor (ER), BET, CDK, HER2, PARP, EZH2, etc. This resource aims to serve as a guide for future PROTAC-based breast cancer treatment design.
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Affiliation(s)
- Zhenjie Wang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China; Office of Drug Clinical Trials, The People's Hospital of Gaozhou, Maoming, 525200, PR China
| | - Siyao Che
- Hepatological Surgery Department, The People's Hospital of Gaozhou, Maoming, 525200, PR China.
| | - Zhiqiang Yu
- Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, PR China.
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Barrera-Ocampo A. Monoclonal antibodies and aptamers: The future therapeutics for Alzheimer's disease. Acta Pharm Sin B 2024; 14:2795-2814. [PMID: 39027235 PMCID: PMC11252463 DOI: 10.1016/j.apsb.2024.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 07/20/2024] Open
Abstract
Alzheimer's disease (AD) is considered the most common and prevalent form of dementia of adult-onset with characteristic progressive impairment in cognition and memory. The cure for AD has not been found yet and the treatments available until recently were only symptomatic. Regardless of multidisciplinary approaches and efforts made by pharmaceutical companies, it was only in the past two years that new drugs were approved for the treatment of the disease. Amyloid beta (Aβ) immunotherapy is at the core of this therapy, which is one of the most innovative approaches looking to change the course of AD. This technology is based on synthetic peptides or monoclonal antibodies (mAb) to reduce Aβ levels in the brain and slow down the advance of neurodegeneration. Hence, this article reviews the state of the art about AD neuropathogenesis, the traditional pharmacologic treatment, as well as the modern active and passive immunization describing approved drugs, and drug prototypes currently under investigation in different clinical trials. In addition, future perspectives on immunotherapeutic strategies for AD and the rise of the aptamer technology as a non-immunogenic alternative to curb the disease progression are discussed.
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Affiliation(s)
- Alvaro Barrera-Ocampo
- Facultad de Ingeniería, Diseño y Ciencias Aplicadas, Departamento de Ciencias Farmacéuticas y Químicas, Grupo Natura, Universidad Icesi, Cali 760031, Colombia
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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 2024:10.1007/s12013-024-01367-w. [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] [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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Chowdhury R, Eslami S, Pham CV, Rai A, Lin J, Hou Y, Greening DW, Duan W. Role of aptamer technology in extracellular vesicle biology and therapeutic applications. NANOSCALE 2024; 16:11457-11479. [PMID: 38856692 DOI: 10.1039/d4nr00207e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Extracellular vesicles (EVs) are cell-derived nanosized membrane-bound vesicles that are important intercellular signalling regulators in local cell-to-cell and distant cell-to-tissue communication. Their inherent capacity to transverse cell membranes and transfer complex bioactive cargo reflective of their cell source, as well as their ability to be modified through various engineering and modification strategies, have attracted significant therapeutic interest. Molecular bioengineering strategies are providing a new frontier for EV-based therapy, including novel mRNA vaccines, antigen cross-presentation and immunotherapy, organ delivery and repair, and cancer immune surveillance and targeted therapeutics. The revolution of EVs, their diversity as biocarriers and their potential to contribute to intercellular communication, is well understood and appreciated but is ultimately dependent on the development of methods and techniques for their isolation, characterization and enhanced targeting. As single-stranded oligonucleotides, aptamers, also known as chemical antibodies, offer significant biological, chemical, economic, and therapeutic advantages in terms of their size, selectivity, versatility, and multifunctional programming. Their integration into the field of EVs has been contributing to the development of isolation, detection, and analysis pipelines associated with bioengineering strategies for nano-meets-molecular biology, thus translating their use for therapeutic and diagnostic utility.
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Affiliation(s)
- Rocky Chowdhury
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
| | - Sadegh Eslami
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
| | - Cuong Viet Pham
- Molecular Imaging and Theranostics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Alin Rai
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Jia Lin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yingchu Hou
- Laboratory of Tumor Molecular and Cellular Biology College of Life Sciences, Shaanxi Normal University 620 West Chang'an Avenue, Xi'an, Shaanxi, 710119, China
| | - David W Greening
- Molecular Proteomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Cardiovascular Research, Translation and Implementation, and La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Wei Duan
- School of Medicine, Deakin University, and IMPACT Strategic Research Centre, Waurn Ponds, VIC, 3216, Australia.
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Santarpia G, Carnes E. Therapeutic Applications of Aptamers. Int J Mol Sci 2024; 25:6742. [PMID: 38928448 PMCID: PMC11204156 DOI: 10.3390/ijms25126742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Affinity reagents, or target-binding molecules, are quite versatile and are major workhorses in molecular biology and medicine. Antibodies are the most famous and frequently used type and they have been used for a wide range of applications, including laboratory techniques, diagnostics, and therapeutics. However, antibodies are not the only available affinity reagents and they do have significant drawbacks, including laborious and costly production. Aptamers are one potential alternative that have a variety of unique advantages. They are single stranded DNA or RNA molecules that can be selected for binding to many targets including proteins, carbohydrates, and small molecules-for which antibodies typically have low affinity. There are also a variety of cost-effective methods for producing and modifying nucleic acids in vitro without cells, whereas antibodies typically require cells or even whole animals. While there are also significant drawbacks to using aptamers in therapeutic applications, including low in vivo stability, aptamers have had success in clinical trials for treating a variety of diseases and two aptamer-based drugs have gained FDA approval. Aptamer development is still ongoing, which could lead to additional applications of aptamer therapeutics, including antitoxins, and combinatorial approaches with nanoparticles and other nucleic acid therapeutics that could improve efficacy.
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Affiliation(s)
- George Santarpia
- College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Eric Carnes
- College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Szymczyk A, Popiołek M, Baran D, Olszewski M, Ziółkowski R, Malinowska E. Aptamer and Electrochemical Aptasensor towards Selenate Ions (SeO 42-). Int J Mol Sci 2024; 25:6660. [PMID: 38928366 PMCID: PMC11203472 DOI: 10.3390/ijms25126660] [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: 05/25/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Selenium is an essential inorganic compound in human and animal nutrition, involved in the proper functioning of the body. As a micronutrient, it actively contributes to the regulation of various metabolic activities, i.e., thyroid hormone, and protection against oxidative stress. However, Se exhibits a narrow concentration window between having a positive effect and exerting a toxic effect. In higher doses, it negatively affects living organisms and causes DNA damage through the formation of free radicals. Increased reactivity of Se anions can also disrupt the integrity and function of DNA-repairing proteins. As the permissible concentration of Se in drinking water is 10 µg/L, it is vital to develop sensitive and robust methods of Se detection in aqueous samples. In this study, for the first time, we proposed a selective aptamer for selenate ion detection, chosen following the SELEX process, and its application in the construction of an electrochemical aptasensor towards SeO42- ions. Measurement conditions such as the used redox marker and pH value of the measurement solution were chosen. The proposed aptasensor is characterized by good selectivity and an LOD of 1 nM. Conditions for biosensor regeneration and storage were also investigated in this research.
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Affiliation(s)
- Anna Szymczyk
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
- Doctoral School, Warsaw University of Technology, Plac Politechniki 1, 00-661 Warsaw, Poland
| | - Martyna Popiołek
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Dominika Baran
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-664 Warsaw, Poland;
| | - Robert Ziółkowski
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
| | - Elżbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland; (A.S.); (M.P.); (D.B.); (E.M.)
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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Daum LT, Rodriguez JD, Chambers JP. Development of Aptamers for RNase Inactivation in Xtract-Free™ Sample Collection and Transport Medium. Diagnostics (Basel) 2024; 14:1207. [PMID: 38928623 PMCID: PMC11203062 DOI: 10.3390/diagnostics14121207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
There is a significant need to develop new environmentally friendly, extraction-free sample collection mediums that can effectively preserve and protect genetic material for point-of-care and/or self-collection, home-collection, and mail-back testing. Systematic evolution of ligands by exponential enrichment (SELEX) was used to create anti-ribonuclease (RNase) deoxyribonucleic acid (DNA) aptamers against purified RNase A conjugated to paramagnetic carboxylated beads. Following eight rounds of SELEX carried out under various stringency conditions, e.g., selection using Xtract-Free™ (XF) specimen collection medium and elevated ambient temperature of 28 °C, a panel of five aptamers was chosen following bioinformatic analysis using next-generation sequencing. The efficacy of aptamer inactivation of RNase was assessed by monitoring ribonucleic acid (RNA) integrity via fluorometric and real-time RT-PCR analysis. Inclusion of aptamers in reaction incubations resulted in an 8800- to 11,200-fold reduction in RNase activity, i.e., digestion of viral RNA compared to control. Thus, anti-RNase aptamers integrated into XF collection medium as well as other commercial reagents and kits have great potential for ensuring quality intact RNA for subsequent genomic analyses.
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Affiliation(s)
- Luke T. Daum
- LuJo BioScience Laboratory, San Antonio, TX 78209, USA;
| | | | - James P. Chambers
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
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Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and identification of DNA nucleic acid aptamers against F1 protein of Yersinia pestis using SELEX method. Mol Biol Rep 2024; 51:722. [PMID: 38829419 DOI: 10.1007/s11033-024-09561-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/16/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Yersinia pestis is a bacterium that causes the disease plague. It has caused the deaths of many people throughout history. The bacterium possesses several virulence factors (pPla, pFra, and PYV). PFra plasmid encodes fraction 1 (F1) capsular antigen. F1 protein protects the bacterium against host immune cells through phagocytosis process. This protein is specific for Y. pestis. Many diagnostic techniques are based on molecular and serological detection and quantification of F1 protein in different food and clinical samples. Aptamers are small nucleic acid sequences that can act as specific ligands for many targets.This study, aimed to isolate the high-affinity ssDNA aptamers against F1 protein. METHODS AND RESULTS In this study, SELEX was used as the main strategy in screening aptamers. Moreover, enzyme-linked aptamer sorbent assay (ELASA) and surface plasmon resonance (SPR) were used to determine the affinity and specificity of obtained aptamers to F1 protein. The analysis showed that among the obtained aptamers, the three aptamers of Yer 21, Yer 24, and Yer 25 were selected with a KD value of 1.344E - 7, 2.004E - 8, and 1.68E - 8 M, respectively. The limit of detection (LoD) was found to be 0.05, 0.076, and 0.033 μg/ml for Yer 21, Yer 24, and Yer 25, respectively. CONCLUSION This study demonstrated that the synthesized aptamers could serve as effective tools for detecting and analyzing the F1 protein, indicating their potential value in future diagnostic applications.
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Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Jafar Amani
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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15
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Urmi R, Banerjee P, Singh M, Singh R, Chhillar S, Sharma N, Chandra A, Singh N, Qamar I. Revolutionizing biomedicine: Aptamer-based nanomaterials and nanodevices for therapeutic applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00843. [PMID: 38881649 PMCID: PMC11179248 DOI: 10.1016/j.btre.2024.e00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
With the progress in two distinct areas of nanotechnology and aptamer identification technologies, the two fields have merged to what is known as aptamer nanotechnology. Aptamers have varying properties in the biomedical field include their small size, non-toxicity, ease of manufacturing, negligible immunogenicity, ability to identify a wide range of targets, and high immobilizing capacity. Nevertheless, aptamers can utilize the distinct characteristics offered by nanomaterials like optical, magnetic, thermal, electronic properties to become more versatile and function as a novel device in diagnostics and therapeutics. This engineered aptamer conjugated nanomaterials, in turn provides a potentially new and unique properties apart from the pre-existing characteristics of aptamer and nanomaterials, where they act to offer wide array of applications in the biomedical field ranging from drug targeting, delivery of drugs, biosensing, bioimaging. This review gives comprehensive insight of the different aptamer conjugated nanomaterials and their utilization in biomedical field. Firstly, it introduces on the aptamer selection methods and roles of nanomaterials offered. Further, different conjugation strategies are explored in addition, the class of aptamer conjugated nanodevices being discussed. Typical biomedical examples and studies specifically, related to drug delivery, biosensing, bioimaging have been presented.
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Affiliation(s)
- Rajkumari Urmi
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Manisha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Risha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Sonam Chhillar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Neha Sharma
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Anshuman Chandra
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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16
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Bisht A, Bhowmik S, Patel P, Gupta GD, Kurmi BD. Aptamer as a targeted approach towards treatment of breast cancer. J Drug Target 2024; 32:510-528. [PMID: 38512151 DOI: 10.1080/1061186x.2024.2333866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Aptamers, a novel type of targeted ligand used in drug delivery, have quickly gained popularity due to their high target specificity and affinity. Different aptamer-mediated drug delivery systems, such as aptamer-drug conjugate (ApDC), aptamer-siRNA, and aptamer-functionalised nanoparticle systems, are currently being developed for the successful treatment of cancer based on the excellent properties of aptamers. These systems can decrease potential toxicity and enhance therapeutic efficacy by targeting the drug moiety. In this review, we provide an overview of recent developments in aptamer-mediated delivery systems for cancer therapy, specifically for breast cancer, and talk about the potential applications and current issues of novel aptamer-based techniques. This study in aptamer technology for breast cancer therapy highlights key aptamers targeting well-established biomarkers such as HER2, oestrogen receptor, and progesterone receptor. Additionally, we explore the potential of aptamers in overcoming various challenges such as drug resistance and improving the delivery of therapeutic agents. This review aims to provide a deeper understanding of the present aptamer-based targeted delivery applications through in-depth analysis to increase efficacy and create new therapeutic approaches that may ultimately lead to better treatment outcomes for cancer patients.
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Affiliation(s)
- Anjali Bisht
- Department of Pharmaceutical Quality Assurance, ISF College Pharmacy, Moga, India
| | | | - Preeti Patel
- Department of Pharmaceutical Chemistry, ISF College Pharmacy, Moga, India
| | | | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College Pharmacy, Moga, India
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17
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Le Dortz LL, Rouxel C, Polack B, Boulouis HJ, Lagrée AC, Deshuillers PL, Haddad N. Tick-borne diseases in Europe: Current prevention, control tools and the promise of aptamers. Vet Parasitol 2024; 328:110190. [PMID: 38714064 DOI: 10.1016/j.vetpar.2024.110190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 04/03/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
In Europe, tick-borne diseases (TBDs) cause significant morbidity and mortality, affecting both human and animal health. Ticks can transmit a wide variety of pathogens (bacteria, viruses, and parasites) and feed on many vertebrate hosts. The incidence and public health burden of TBDs are tending to intensify in Europe due to various factors, mainly anthropogenic and often combined. Early detection of tick-borne pathogens (TBPs), preventive measures and treatment are of great importance to control TBDs and their expansion. However, there are various limitations in terms of the sensitivity and/or specificity of detection and prevention methods, and even in terms of feasibility. Aptamers are single-stranded DNA or RNA that could address these issues as they are able to bind with high affinity and specificity to a wide range of targets (e.g., proteins, small compounds, and cells) due to their unique three-dimensional structure. To date, aptamers have been selected against TBPs such as tick-borne encephalitis virus, Francisella tularensis, and Rickettsia typhi. These studies have demonstrated the benefits of aptamer-based assays for pathogen detection and medical diagnosis. In this review, we address the applications of aptamers to TBDs and discuss their potential for improving prevention measures (use of chemical acaricides, vaccination), diagnosis and therapeutic strategies to control TBDs.
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Affiliation(s)
- Lisa Lucie Le Dortz
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Clotilde Rouxel
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Bruno Polack
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Henri-Jean Boulouis
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Anne-Claire Lagrée
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Pierre Lucien Deshuillers
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France
| | - Nadia Haddad
- ANSES, INRAE, EnvA (Ecole nationale vétérinaire d'Alfort), UMR BIPAR, Laboratory of Animal Health, Maisons-Alfort F-94700, France.
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Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
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Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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19
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Presela R, Prabu SS, Ch'ng ES, Tang TH, Citartan M. The diagnostic potentiality of the RNA aptamer against progesterone receptor isolated by crush and soak (CRUSOAK)-SELEX. Mikrochim Acta 2024; 191:346. [PMID: 38802696 DOI: 10.1007/s00604-024-06423-z] [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: 02/09/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Aptamers are a class of molecular recognition elements that exhibit high binding affinity and specificity against their respective targets. In view of the many advantages aptamers harbor over their counterpart antibodies, we were impelled to isolate an RNA aptamer against progesterone receptor, particularly its DNA binding domain. A total of eight SELEX cycles were executed against the recombinant Progesterone Receptor DNA-binding domain (PR DBD). The RNA-protein complex in the gel shift assay was subjected to crush and soak method to elute the binders prior to conventional sequencing, the step of which was based upon to coin the term CRUSOAK-SELEX. The sequencing revealed three different classes of sequences, with one class termed, PRapt-3, showing the strongest binding against PR DBD. The dissociation constant of PRapt-3 RNA aptamer was estimated at 380 nM ± 35 nM. PRapt-3 was successfully used to develop aptamer-based diagnostic assays such as ELASA, aptamer-based dot blot, and aptamer-based western blot. The prominent highlight is the performance of the aptamer in aptacytostaining, which was unachievable with antibodies. Compared to its counterpart antibodies, PRapt-3 has a better penetration capacity in aptahistostaining using the formalin-fixed paraffin-embedded (FFPE) breast cancer cells and tissue blocks. This study represents the first ever demonstration of an aptamer against progesterone receptor and its diagnostic capacity.
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Affiliation(s)
- Ravinderan Presela
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Siva Sankar Prabu
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ewe Seng Ch'ng
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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20
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Oliveira R, Pinho E, Barros MM, Azevedo NF, Almeida C. In vitro selection of DNA aptamers against staphylococcal enterotoxin A. Sci Rep 2024; 14:11345. [PMID: 38762575 PMCID: PMC11102521 DOI: 10.1038/s41598-024-61094-3] [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: 12/29/2022] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
Staphylococcal enterotoxin A (SEA) is the most frequently reported in staphylococcal food poisoning (SFP) outbreaks. Aptamers are single-stranded nucleic acids that are seen as promising alternatives to antibodies in several areas, including diagnostics. In this work, systematic evolution of ligands by exponential enrichment (SELEX) was used to select DNA aptamers against SEA. The SELEX protocol employed magnetic beads as an immobilization matrix for the target molecule and real-time quantitative PCR (qPCR) for monitoring and optimizing sequence enrichment. After 10 selection cycles, the ssDNA pool with the highest affinity was sequenced by next generation sequencing (NGS). Approximately 3 million aptamer candidates were identified, and the most representative cluster sequences were selected for further characterization. The aptamer with the highest affinity showed an experimental dissociation constant (KD) of 13.36 ± 18.62 nM. Increased temperature negatively affected the affinity of the aptamer for the target. Application of the selected aptamers in a lateral flow assay demonstrated their functionality in detecting samples containing 100 ng SEA, the minimum amount capable of causing food poisoning. Overall, the applicability of DNA aptamers in SEA recognition was demonstrated and characterized under different conditions, paving the way for the development of diagnostic tools.
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Affiliation(s)
- Ricardo Oliveira
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal.
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
| | - Eva Pinho
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Maria Margarida Barros
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Vairão, 4485-655, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- AliCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Eigenfeld M, Lupp KFM, Schwaminger SP. Role of Natural Binding Proteins in Therapy and Diagnostics. Life (Basel) 2024; 14:630. [PMID: 38792650 PMCID: PMC11122601 DOI: 10.3390/life14050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.
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Affiliation(s)
- Marco Eigenfeld
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kilian F. M. Lupp
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sebastian P. Schwaminger
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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Li Y, Qian M, Liu Y, Qiu X. APPROACH: Sensitive Detection of Exosomal Biomarkers by Aptamer-Mediated Proximity Ligation Assay and Time-Resolved Förster Resonance Energy Transfer. BIOSENSORS 2024; 14:233. [PMID: 38785707 PMCID: PMC11117858 DOI: 10.3390/bios14050233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Exosomal biomarker detection holds great importance in the field of in vitro diagnostics, offering a non-invasive and highly sensitive approach for early disease detection and personalized treatment. Here, we proposed an "APPROACH" strategy, combining aptamer-mediated proximity ligation assay (PLA) with rolling circle amplification (RCA) and time-resolved Förster resonance energy transfer (TR-FRET) for the sensitive and semi-homogenous detection of exosomal biomarkers. PLA probes consisted of a cholesterol-conjugated oligonucleotide, which anchored to the membrane of an exosome, and a specific aptamer oligonucleotide that recognized a target protein of the exosome; the proximal binding of pairs of PLA probes to the same exosome positioned the oligonucleotides in the vicinity of each other, guiding the hybridization and ligation of two subsequently added backbone and connector oligonucleotides to form a circular DNA molecule. Circular DNA formed from PLA underwent rolling circle amplification (RCA) for signal amplification, and the resulting RCA products were subsequently quantified by TR-FRET. The limits of detection provided by APPROACH for the exosomal biomarkers CD63, PD-L1, and HER2 were 0.46 ng∙μL-1, 0.77 ng∙μL-1, and 1.1 ng∙μL-1, respectively, demonstrating excellent analytical performance with high sensitivity and quantification accuracy. Furthermore, the strategy afforded sensitive detection of exosomal CD63 with a LOD of 1.56 ng∙μL-1 in complex biological matrices, which underscored its anti-interference capability and potential for in vitro detection. The proposed strategy demonstrates wide-ranging applicability in quantifying diverse exosomal biomarkers while exhibiting robust analytical characteristics, including high sensitivity and accuracy.
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Affiliation(s)
- Ying Li
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | - Meiqi Qian
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | | | - Xue Qiu
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
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Yang ZH, Huang LF, Wang YS, Chang CC. Turn-off enzyme activity of histidine-rich peptides for the detection of lysozyme. Mikrochim Acta 2024; 191:307. [PMID: 38713296 DOI: 10.1007/s00604-024-06388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
An assay that integrates histidine-rich peptides (HisRPs) with high-affinity aptamers was developed enabling the specific and sensitive determination of the target lysozyme. The enzyme-like activity of HisRP is inhibited by its interaction with a target recognized by an aptamer. In the presence of the target, lysozyme molecules progressively assemble on the surface of HisRP in a concentration-dependent manner, resulting in the gradual suppression of enzyme-like activity. This inhibition of HisRP's enzyme-like activity can be visually observed through color changes in the reaction product or quantified using UV-visible absorption spectroscopy. Under optimal conditions, the proposed colorimetric assay for lysozyme had a detection limit as low as 1 nM and exhibited excellent selectivity against other nonspecific interferents. Furthermore, subsequent research validated the practical applicability of the developed colorimetric approach to saliva samples, indicating that the assay holds significant potential for the detection of lysozymes in samples derived from humans.
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Affiliation(s)
- Zu-Han Yang
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan
| | - Ling-Fang Huang
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 333, Taiwan
| | - Yi-Shan Wang
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 333, Taiwan
| | - Chia-Chen Chang
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, 333, Taiwan.
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, 333, Taiwan.
- Kidney Research Center, Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, 333, Taiwan.
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24
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Zeng Z, Li W, Zhang J, Hu Z, Wu J, Ye G, Luo Y. Highly sensitive and specific graphene oxide-based FRET aptasensor for quantitative detection of human soluble growth stimulating gene protein 2. Talanta 2024; 271:125629. [PMID: 38245955 DOI: 10.1016/j.talanta.2024.125629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
Soluble growth stimulation expressed gene 2 (sST2) is a new generation biomarker in the diagnosis and prognosis of heart failure (HF). Here, the sST2-specific aptamers were selected from a random ssDNA library with the full length of 88 nucleotides (nt) via target-immobilized magnetic beads (MB)-based systematic evolution of ligands by exponential enrichment (SELEX) technology. After eight rounds of selection, six aptamers with the most enrichment were selected. Among, the aptamer L1 showed the high-affinity binding to sST2 with the lowest Kd value (77.3 ± 0.05 nM), which was chosen as the optimal aptamer for further molecular docking. Then, the aptamer L1 was used to construct a graphene oxide (GO) - based fluorescence resonance energy transfer (FRET) biosensor for sST2, which exhibits a linear detection range of 0.1-100 μg/ml and a detection limit of 3.7 ng/ml. The aptasensor was applied to detect sST2 in real samples, with a good correlation and agreement with the traditional enzyme-linked immunosorbent assay (ELISA) when quantitative analyzing the sST2 concentration in serum samples from HF patients. The results show that not only an efficient strategy for screening the practicable aptamer, but also a rapid and sensitive detection platform for sST2 were established.
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Affiliation(s)
- Zhikun Zeng
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenfeng Li
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jixuan Zhang
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Zijian Hu
- The First Clinical College of Wuhan University, Wuhan, 430060, Hubei, China
| | - Junyi Wu
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Guangming Ye
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Yi Luo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
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Hsu SH, Yang HY, Chang CC, Tsai SK, Li C, Chang MY, Ko YC, Chou LF, Tsai CY, Tian YC, Yang CW. Blocking pathogenic Leptospira invasion with aptamer molecules targeting outer membrane LipL32 protein. Microbes Infect 2024; 26:105299. [PMID: 38224944 DOI: 10.1016/j.micinf.2024.105299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
This study aimed to develop aptamers targeting LipL32, a most abundant lipoprotein in pathogenic Leptospira, to hinder bacterial invasion. The objectives were to identify high-affinity aptamers through SELEX and evaluate their specificity and inhibitory effects. SELEX was employed to generate LipL32 aptamers (L32APs) over 15 rounds of selection. L32APs' binding affinity and specificity for pathogenic Leptospira were assessed. Their ability to inhibit LipL32-ECM interaction and Leptospira invasion was investigated. Animal studies were conducted to evaluate the impact of L32AP treatment on survival rates, Leptospira colonization, and kidney damage. Three L32APs with strong binding affinity were identified. They selectively detected pathogenic Leptospira, sparing non-pathogenic strains. L32APs inhibited LipL32-ECM interaction and Leptospira invasion. In animal studies, L32AP administration significantly improved survival rates, reduced Leptospira colonies, and mitigated kidney damage compared to infection alone. This pioneering research developed functional aptamers targeting pathogenic Leptospira. The identified L32APs exhibited high affinity, pathogen selectivity, and inhibition of invasion and ECM interaction. L32AP treatment showed promising results, enhancing survival rates and reducing Leptospira colonization and kidney damage. These findings demonstrate the potential of aptamers to impede pathogenic Leptospira invasion and aid in recovery from Leptospira-induced kidney injury (190 words).
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Affiliation(s)
- Shen-Hsing Hsu
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
| | - Huang-Yu Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chia-Chen Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | | | - Chien Li
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ming-Yang Chang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ching Ko
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Li-Fang Chou
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chung-Ying Tsai
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ya-Chung Tian
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Wei Yang
- Kidney Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Léguillier V, Heddi B, Vidic J. Recent Advances in Aptamer-Based Biosensors for Bacterial Detection. BIOSENSORS 2024; 14:210. [PMID: 38785684 PMCID: PMC11117931 DOI: 10.3390/bios14050210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
The rapid and sensitive detection of pathogenic bacteria is becoming increasingly important for the timely prevention of contamination and the treatment of infections. Biosensors based on nucleic acid aptamers, integrated with optical, electrochemical, and mass-sensitive analytical techniques, have garnered intense interest because of their versatility, cost-efficiency, and ability to exhibit high affinity and specificity in binding bacterial biomarkers, toxins, and whole cells. This review highlights the development of aptamers, their structural characterization, and the chemical modifications enabling optimized recognition properties and enhanced stability in complex biological matrices. Furthermore, recent examples of aptasensors for the detection of bacterial cells, biomarkers, and toxins are discussed. Finally, we explore the barriers to and discuss perspectives on the application of aptamer-based bacterial detection.
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Affiliation(s)
- Vincent Léguillier
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Brahim Heddi
- ENS Paris-Saclay, Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, 91190 Gif-sur-Yvette, France
| | - Jasmina Vidic
- INRAE, AgroParisTech, Micalis Institut, Université Paris-Saclay, UMR 1319, 78350 Jouy-en-Josas, France;
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27
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Zhang Y, Yu W, Zhang L, Li P. Nanozyme-based visual diagnosis and therapeutics for myocardial infarction: The application and strategy. J Adv Res 2024:S2090-1232(24)00162-0. [PMID: 38657902 DOI: 10.1016/j.jare.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Myocardial infarction (MI) is a heart injury caused by ischemia and low oxygen conditions. The occurrence of MI lead to the activation of a large number of neutrophils and macrophages, inducing severe inflammatory injury. Meanwhile, the inflammatory response produces much more free radicals, further exacerbating the inflammatory response and tissue damage. Efforts are being dedicated to developing antioxidants and enzymes, as well as small molecule drugs, for treating myocardial ischemia. However, poor pharmacokinetics and potential side effects limit the clinical application of these drugs. Recent advances in nanotechnology have paved new pathways in biomedical and healthcare environments. Nanozymes exhibit the advantages of biological enzymes and nanomaterials, including with higher catalytic activity and stability than natural enzymes. Thus, nanozymes provide new possibilities for the diagnosis and treatment of oxidative stress and inflammation-related diseases. AIM OF REVIEW We describe the application of nanozymes in the diagnosis and therapy of MI, aiming to bridge the gap between the diagnostic and therapeutic needs of MI. KEY SCIENTIFIC CONCEPTS OF REVIEW We describe the application of nanozymes in the diagnosis and therapy of MI, and discuss the new strategies for improving the diagnosis and treatment of MI. We review in detail the applications of nanozymes to achieve highly sensitive detection of biomarkers of MI. Due to their unique enzyme catalytic capabilities, nanozymes have the ability to sensitively detect biomolecules through colorimetric, fluorescent, and electrochemical assays. In addition, nanozymes exhibit excellent antioxidase-mimicking activity to treat MI by modulating reduction/oxidation (REDOX) homeostasis. Nanozymes can also passively or actively target MI tissue sites, thereby protecting ischemic myocardial tissue and reducing the infarct area. These innovative applications of nanozymes in the field of biomedicine have shown promising results in the diagnosis and treatment of MI, offering a novel therapeutic strategy.
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Affiliation(s)
- Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Wanpeng Yu
- Medical Collage, Qingdao University, Qingdao, China
| | - Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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28
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Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [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: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
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Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
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29
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Araújo D, Silva AR, Fernandes R, Serra P, Barros MM, Campos AM, Oliveira R, Silva S, Almeida C, Castro J. Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals. Pathogens 2024; 13:320. [PMID: 38668275 PMCID: PMC11054384 DOI: 10.3390/pathogens13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
The importance of addressing the problem of biofilms in farm, wild, and companion animals lies in their pervasive impact on animal health and welfare. Biofilms, as resilient communities of microorganisms, pose a persistent challenge in causing infections and complicating treatment strategies. Recognizing and understanding the importance of mitigating biofilm formation is critical to ensuring the welfare of animals in a variety of settings, from farms to the wild and companion animals. Effectively addressing this issue not only improves the overall health of individual animals, but also contributes to the broader goals of sustainable agriculture, wildlife conservation, and responsible pet ownership. This review examines the current understanding of biofilm formation in animal diseases and elucidates the complex processes involved. Recognizing the limitations of traditional antibiotic treatments, mechanisms of resistance associated with biofilms are explored. The focus is on alternative therapeutic strategies to control biofilm, with illuminating case studies providing valuable context and practical insights. In conclusion, the review highlights the importance of exploring emerging approaches to mitigate biofilm formation in animals. It consolidates existing knowledge, highlights gaps in understanding, and encourages further research to address this critical facet of animal health. The comprehensive perspective provided by this review serves as a foundation for future investigations and interventions to improve the management of biofilm-associated infections in diverse animal populations.
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Affiliation(s)
- Daniela Araújo
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Ana Rita Silva
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Rúben Fernandes
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Patrícia Serra
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Maria Margarida Barros
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Ana Maria Campos
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
| | - Ricardo Oliveira
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- AliCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Sónia Silva
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Carina Almeida
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- AliCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana Castro
- INIAV—National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vila do Conde, Portugal; (A.R.S.); (R.F.); (P.S.); (M.M.B.); (A.M.C.); (R.O.); (S.S.); (C.A.)
- CEB—Centre of Biological Engineering Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
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Manea I, Casian M, Hosu-Stancioiu O, de-Los-Santos-Álvarez N, Lobo-Castañón MJ, Cristea C. A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules. Anal Chim Acta 2024; 1297:342325. [PMID: 38438246 DOI: 10.1016/j.aca.2024.342325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/06/2024]
Abstract
This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.
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Affiliation(s)
- Ioana Manea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania
| | - Magdolna Casian
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania; Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain
| | - Oana Hosu-Stancioiu
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
| | - Noemí de-Los-Santos-Álvarez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. de Roma s/n, 33011, Oviedo, Spain
| | - Cecilia Cristea
- Department of Analytical Chemistry, Faculty of Pharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, 4 Pasteur Street, 400349, Cluj-Napoca, Romania.
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31
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Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW. Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. Molecules 2024; 29:1124. [PMID: 38474636 DOI: 10.3390/molecules29051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.
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Affiliation(s)
- Bang Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Firas Kobeissy
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
| | - Mojtaba Golpich
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Guangzheng Cai
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Xiaowei Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Reem Abedi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107-2020, Lebanon
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, China
| | - Steven A Benner
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Kevin K W Wang
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
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Toma L, Mattarozzi M, Ronda L, Marassi V, Zattoni A, Fortunati S, Giannetto M, Careri M. Are Aptamers Really Promising as Receptors for Analytical Purposes? Insights into Anti-Lysozyme DNA Aptamers through a Multitechnique Study. Anal Chem 2024; 96:2719-2726. [PMID: 38294352 DOI: 10.1021/acs.analchem.3c05883] [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: 02/01/2024]
Abstract
Aptamers are recognition elements increasingly used for the development of biosensing strategies, especially in the detection of proteins or small molecule targets. Lysozyme, which is recognized as an important biomarker for various diseases and a major allergenic protein found in egg whites, is one of the main analytical targets of aptamer-based biosensors. However, since aptamer-based strategies can be prone to artifacts and data misinterpretation, rigorous strategies for multifaceted characterization of the aptamer-target interaction are needed. In this work, a multitechnique approach has been devised to get further insights into the binding performance of the anti-lysozyme DNA aptamers commonly used in the literature. To study molecular interactions between lysozyme and different anti-lysozyme DNA aptamers, measurements based on a magneto-electrochemical apta-assay, circular dichroism spectroscopy, fluorescence spectroscopy, and asymmetrical flow field-flow fractionation were performed. The reliability and versatility of the approach were proved by investigating a SELEX-selected RNA aptamer reported in the literature, that acts as a positive control. The results confirmed that an interaction in the low micromolar range is present in the investigated binding buffers, and the binding is not associated with a conformational change of either the protein or the DNA aptamer. The similar behavior of the anti-lysozyme DNA aptamers compared to that of randomized sequences and polythymine, used as negative controls, showed nonsequence-specific interactions. This study demonstrates that severe testing of aptamers resulting from SELEX selection is the unique way to push these biorecognition elements toward reliable and reproducible results in the analytical field.
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Affiliation(s)
- Lorenzo Toma
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- CNR, Institute of Biophysics, Pisa 56124, Italy
| | - Valentina Marassi
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Andrea Zattoni
- Department of Chemistry, University of Bologna, Via Selmi 2, Bologna 40126, Italy
- byFlow srl, Bologna 40126, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Simone Fortunati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Marco Giannetto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parma 43124, Italy
- INBB, National Institute for Biostructures and Biosystems, Rome 00136 , Italy
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KÜÇÜKCANKURT F, UÇAK S, ALTIOK N. Theranostic potential of a novel aptamer specifically targeting HER2 in breast cancer cells. Turk J Biol 2024; 48:35-45. [PMID: 38665781 PMCID: PMC11042868 DOI: 10.55730/1300-0152.2680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/27/2024] [Accepted: 02/01/2024] [Indexed: 04/28/2024] Open
Abstract
Background/aim The overexpression of HER2 is correlated with poorer outcomes and therapeutic resistance in breast cancer patients. While HER2-targeted therapies have shown improvement, prognosis remains poor for HER2-positive breast cancer patients, and these treatments have limitations. Therefore, it is crucial to explore effective molecular strategies for early detection and treatment of HER2-positive breast cancers. Materials and methods In this study, we employed the cell-SELEX method to generate a selective aptamer capable of recognizing HER2 in its native conformation within breast cancer cells, for theranostic applications. Utilizing an adherent cell-SELEX approach, we developed and explored a DNA aptamer, named HMAP7, which can specifically target HER2 in the MDA-MB-453 and SK-BR-3 human breast cancer cell lines. After sequencing, the binding affinities of 10 candidate aptamers to HER2 receptors were evaluated by measuring fluorescence intensities within intact cells using near-infrared optical imaging. The dissociation constant of HMAP7 was determined to be in the nanomolar range in both cell lines. Results The cell-SELEX-derived aptamer sequence, HMAP7 (41-mer), exhibited the highest binding affinity and specificity for HER2. HMAP7 was rapidly internalized into breast cancer cells overexpressing HER2 but showed no uptake in the HER2 receptor-deficient breast cancer cell line MDA-MB-231. Moreover, HMAP7 demonstrated remarkable selectivity for HER2, rendering it suitable for use in complex biological systems. Conclusions Our findings suggest that the novel DNA aptamer HMAP7 holds promise for both therapeutic and diagnostic applications, enabling selective delivery of therapeutic agents or imaging of HER2-positive breast tumors.
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Affiliation(s)
- Fulya KÜÇÜKCANKURT
- Department of Medical Biology, School of Medicine, Altinbas University, İstanbul,
Turkiye
| | - Samet UÇAK
- Department of Medical Biology, School of Medicine, Istanbul Aydin University, İstanbul,
Turkiye
| | - Nedret ALTIOK
- Department of Pharmacology and Medical Pharmacology, School of Medicine, Istinye University, İstanbul,
Turkiye
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Chowdhury MA, Collins JM, Gell DA, Perry S, Breadmore MC, Shigdar S, King AE. Isolation and Identification of the High-Affinity DNA Aptamer Target to the Brain-Derived Neurotrophic Factor (BDNF). ACS Chem Neurosci 2024; 15:346-356. [PMID: 38149631 DOI: 10.1021/acschemneuro.3c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Aptamers are functional oligonucleotide ligands used for the molecular recognition of various targets. The natural characteristics of aptamers make them an excellent alternative to antibodies in diagnostics, therapeutics, and biosensing. DNA aptamers are mainly single-stranded oligonucleotides (ssDNA) that possess a definite binding to targets. However, the application of aptamers to the fields of brain health and neurodegenerative diseases has been limited to date. Herein, a DNA aptamer against the brain-derived neurotrophic factor (BDNF) protein was obtained by in vitro selection. BDNF is a potential biomarker of brain health and neurodegenerative diseases and has functions in the synaptic plasticity and survival of neurons. We identified eight aptamers that have binding affinity for BDNF from a 50-nucleotide library. Among these aptamers, NV_B12 showed the highest sensitivity and selectivity for detecting BDNF. In an aptamer-linked immobilized sorbent assay (ALISA), the NV_B12 aptamer strongly bound to BDNF protein, in a dose-dependent manner. The dissociation constant (Kd) for NV_B12 was 0.5 nM (95% CI: 0.4-0.6 nM). These findings suggest that BDNF-specific aptamers could be used as an alternative to antibodies in diagnostic and detection assays for BDNF.
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Affiliation(s)
- Md Anisuzzaman Chowdhury
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Jessica M Collins
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - David A Gell
- Menzies Research Institute, School of Medicine, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Michael C Breadmore
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Sandy Bay, Hobart, Tasmania 7001, Australia
| | - Sarah Shigdar
- School of Medicine, Faculty of Health, Deakin University, Geelong, Victoria 3220, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
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Wang X, Jia B, Lee K, Davis B, Wen C, Wang Y, Zheng H, Wang Y. Biomimetic Bacterial Capsule for Enhanced Aptamer Display and Cell Recognition. J Am Chem Soc 2024; 146:868-877. [PMID: 38153404 DOI: 10.1021/jacs.3c11208] [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: 12/29/2023]
Abstract
Great effort has been made to encapsulate or coat living mammalian cells for a variety of applications ranging from diabetes treatment to three-dimensional printing. However, no study has reported the synthesis of a biomimetic bacterial capsule to display high-affinity aptamers on the cell surface for enhanced cell recognition. Therefore, we synthesized an ultrathin alginate-polylysine coating to display aptamers on the surface of living cells with natural killer (NK) cells as a model. The results show that this coating-mediated aptamer display is more stable than direct cholesterol insertion into the lipid bilayer. The half-life of the aptamer on the cell surface can be increased from less than 1.5 to over 20 h. NK cells coated with the biomimetic bacterial capsule exhibit a high efficiency in recognizing and killing target cells. Therefore, this work has demonstrated a promising cell coating method for the display of aptamers for enhanced cell recognition.
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Affiliation(s)
- Xuelin Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bei Jia
- Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Connie Wen
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yixun Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hong Zheng
- Penn State Cancer Institute, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
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Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Wong KY, Wong MS, Liu J. Aptamer-functionalized liposomes for drug delivery. Biomed J 2023:100685. [PMID: 38081386 DOI: 10.1016/j.bj.2023.100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/21/2023] [Accepted: 12/05/2023] [Indexed: 07/26/2024] Open
Abstract
Among the various targeting ligands for drug delivery, aptamers have attracted much interest in recent years because of their smaller size compared to antibodies, ease of modification, and better batch-to-batch consistency. In addition, aptamers can be selected to target both known and even unknown cell surface biomarkers. For drug loading, liposomes are the most successful vehicle and many FDA-approved formulations are based on liposomes. In this paper, aptamer-functionalized liposomes for targeted drug delivery are reviewed. We begin with the description of related aptamers selection, followed by methods to conjugate aptamers to liposomes and the fate of such conjugates in vivo. Then a few examples of applications are reviewed. In addition to intravenous injection for systemic delivery and hoping to achieve accumulation at target sites, for certain applications, it is also possible to have aptamer/liposome conjugates applied directly at the target tissue such as intratumor injection and dropping on the surface of the eye by adhering to the cornea. While previous reviews have focused on cancer therapy, the current review mainly covers other applications in the last four years. Finally, this article discusses potential issues of aptamer targeting and some future research opportunities.
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Affiliation(s)
- Ka-Ying Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada; Centre for Eye and Vision Research (CEVR), Hong Kong.
| | - Man-Sau Wong
- Centre for Eye and Vision Research (CEVR), Hong Kong; Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong; Research Center for Chinese Medicine Innovation, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Canada; Centre for Eye and Vision Research (CEVR), Hong Kong.
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Rousseau CR, Kumakli H, White RJ. Perspective-Assessing Electrochemical, Aptamer-Based Sensors for Dynamic Monitoring of Cellular Signaling. ECS SENSORS PLUS 2023; 2:042401. [PMID: 38152504 PMCID: PMC10750225 DOI: 10.1149/2754-2726/ad15a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
Electrochemical, aptamer-based (E-AB) sensors provide a generalizable strategy to quantitatively detect a variety of targets including small molecules and proteins. The key signaling attributes of E-AB sensors (sensitivity, selectivity, specificity, and reagentless and dynamic sensing ability) make them well suited to monitor dynamic processes in complex environments. A key bioanalytical challenge that could benefit from the detection capabilities of E-AB sensors is that of cell signaling, which involves the release of molecular messengers into the extracellular space. Here, we provide a perspective on why E-AB sensors are suited for this measurement, sensor requirements, and pioneering examples of cellular signaling measurements.
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Affiliation(s)
- Celeste R. Rousseau
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| | - Hope Kumakli
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio 45221, United States of America
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Nasaev SS, Mukanov AR, Kuznetsov II, Veselovsky AV. AliNA - a deep learning program for RNA secondary structure prediction. Mol Inform 2023; 42:e202300113. [PMID: 37710142 DOI: 10.1002/minf.202300113] [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: 05/14/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Nowadays there are numerous discovered natural RNA variations participating in different cellular processes and artificial RNA, e. g., aptamers, riboswitches. One of the required tasks in the investigation of their functions and mechanism of influence on cells and interaction with targets is the prediction of RNA secondary structures. The classic thermodynamic-based prediction algorithms do not consider the specificity of biological folding and deep learning methods that were designed to resolve this issue suffer from homology-based methods problems. Herein, we present a method for RNA secondary structure prediction based on deep learning - AliNA (ALIgned Nucleic Acids). Our method successfully predicts secondary structures for non-homologous to train-data RNA families thanks to usage of the data augmentation techniques. Augmentation extends existing datasets with easily-accessible simulated data. The proposed method shows a high quality of prediction across different benchmarks including pseudoknots. The method is available on GitHub for free (https://github.com/Arty40m/AliNA).
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Affiliation(s)
- Shamsudin S Nasaev
- Institute of Biomedical Chemistry, 10, Pogodinskaya str., 119121, Moscow, Russia
| | - Artem R Mukanov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008, Kazan, Russia
| | - Ivan I Kuznetsov
- Moscow University of Finance and Law, 10 block 1, Serpuhovsky val str., 115191, Moscow, Russia
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Shin I, Kang K, Kim J, Sel S, Choi J, Lee JW, Kang HY, Song G. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders. BMC Bioinformatics 2023; 24:447. [PMID: 38012571 PMCID: PMC10680337 DOI: 10.1186/s12859-023-05577-6] [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: 08/24/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evolution of ligands by exponential enrichment (SELEX) method is a critical in vitro technique employed to identify aptamers that bind specifically to target proteins. While advanced SELEX-based methods such as Cell- and HT-SELEX are available, they often encounter issues such as extended time consumption and suboptimal accuracy. Several In silico aptamer discovery methods have been proposed to address these challenges. These methods are specifically designed to predict aptamer-protein interaction (API) using benchmark datasets. However, these methods often fail to consider the physicochemical interactions between aptamers and proteins within tertiary structures. RESULTS In this study, we propose AptaTrans, a pipeline for predicting API using deep learning techniques. AptaTrans uses transformer-based encoders to handle aptamer and protein sequences at the monomer level. Furthermore, pretrained encoders are utilized for the structural representation. After validation with a benchmark dataset, AptaTrans has been integrated into a comprehensive toolset. This pipeline synergistically combines with Apta-MCTS, a generative algorithm for recommending aptamer candidates. CONCLUSION The results show that AptaTrans outperforms existing models for predicting API, and the efficacy of the AptaTrans pipeline has been confirmed through various experimental tools. We expect AptaTrans will enhance the cost-effectiveness and efficiency of SELEX in drug discovery. The source code and benchmark dataset for AptaTrans are available at https://github.com/pnumlb/AptaTrans .
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Affiliation(s)
- Incheol Shin
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Keumseok Kang
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Juseong Kim
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Sanghun Sel
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jeonghoon Choi
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea
| | - Jae-Wook Lee
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Ho Young Kang
- Research & Development, NuclixBio, Seoul, Republic of Korea
| | - Giltae Song
- Division of Artificial Intelligence, Pusan National University, Busan, Republic of Korea.
- School of Computer Science and Engineering, Pusan National University, Busan, Republic of Korea.
- Center for Artificial Intelligence Research, Pusan National University, Busan, Republic of Korea.
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Lin Y, Chen CY, Ku YC, Wang LC, Hung CC, Lin ZQ, Chen BH, Hung JT, Sun YC, Hung KF. A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen. RSC Adv 2023; 13:32681-32693. [PMID: 37936644 PMCID: PMC10626974 DOI: 10.1039/d3ra04686a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
Aptamers have sparked significant interest in cell recognition because of their superior binding specificity and biocompatibility. Cell recognition can be mediated by targeting the major histocompatibility complex (MHC) that presents short peptides derived from intracellular antigens. Although numerous antibodies have demonstrated a specific affinity for the peptide-MHC complex, the number of aptamers that exhibit comparable characteristics is limited. Aptamers are usually selected from large libraries via the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), an iterative process of selection and PCR amplification to enrich a pool of aptamers with high affinity. However, the success rate of aptamer identification is low, possibly due to the presence of complementary sequences or sequences rich in guanine and cytosine that are less accessible for primers. Here, we modified SELEX by employing systemic consecutive selections with minimal PCR amplification. We also modified the analysis by selecting aptamers that were identified in multiple selection rounds rather than those that are highly enriched. Using this approach, we were able to identify two aptamers with binding specificity to cells expressing the ovalbumin alloantigen as a proof of concept. These two aptamers were also discovered among the top 150 abundant candidates, despite not being highly enriched, by performing conventional SELEX. Additionally, we found that highly enriched aptamers tend to contain fractions of the primer sequence and have minimal target affinity. Candidate aptamers are easily missed in the conventional SELEX process. Therefore, our modification for SELEX may facilitate the identification of aptamers for more application in diverse biomedical fields. Significance: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that this approach is particularly useful to select aptamers that can selectively bind to cells presenting a particular peptide by the major histocompatibility complex (MHC) on the cell surface. Given that cancer cells may express mutant peptide-MHC complexes that are distinct from those expressed by normal cells, this study sheds light on the potential application of aptamers to cancer cell targeting.
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Affiliation(s)
- Yang Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yu-Chia Ku
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Li-Chin Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chia-Chien Hung
- School of Computer Science, Georgia Institute of Technology Atlanta GA USA
| | - Zhi-Qian Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Bing-Hong Chen
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | | | - Yi-Chen Sun
- School of Medicine, Tzu-Chi University Hualien Taiwan
- Department of Ophthalmology, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City Taiwan
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University Taipei Taiwan
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Lee M, Shin S, Kim S, Park N. Recent Advances in Biological Applications of Aptamer-Based Fluorescent Biosensors. Molecules 2023; 28:7327. [PMID: 37959747 PMCID: PMC10647268 DOI: 10.3390/molecules28217327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Aptamers have been spotlighted as promising bio-recognition elements because they can be tailored to specific target molecules, bind to targets with a high affinity and specificity, and are easy to chemically synthesize and introduce functional groups to. In particular, fluorescent aptasensors are widely used in biological applications to diagnose diseases as well as prevent diseases by detecting cancer cells, viruses, and various biomarkers including nucleic acids and proteins as well as biotoxins and bacteria from food because they have the advantages of a high sensitivity, selectivity, rapidity, a simple detection process, and a low price. We introduce screening methods for isolating aptamers with q high specificity and summarize the sequences and affinities of the aptamers in a table. This review focuses on aptamer-based fluorescence detection sensors for biological applications, from fluorescent probes to mechanisms of action and signal amplification strategies.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (M.L.); (S.K.)
| | - Seonhye Shin
- Department of Chemistry, The Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea;
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea; (M.L.); (S.K.)
| | - Nokyoung Park
- Department of Chemistry, The Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea;
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Ding Y, Liu J. Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers. Anal Chem 2023; 95:14651-14658. [PMID: 37721984 DOI: 10.1021/acs.analchem.3c02477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Cha BS, Jang YJ, Lee ES, Kim DY, Woo JS, Son J, Kim S, Shin J, Han J, Kim S, Park KS. Development of a Novel DNA Aptamer Targeting Colorectal Cancer Cell-Derived Small Extracellular Vesicles as a Potential Diagnostic and Therapeutic Agent. Adv Healthc Mater 2023; 12:e2300854. [PMID: 37129521 DOI: 10.1002/adhm.202300854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Indexed: 05/03/2023]
Abstract
Colorectal cancer (CRC) as the second leading cause of global cancer deaths poses critical challenges in clinical settings. Cancer-derived small extracellular vesicles (sEVs), which are secreted by cancer cells, have been shown to mediate tumor development, invasion, and even metastasis, and have thus received increasing attention for the development of cancer diagnostic or therapeutic platforms. In the present study, the sEV-targeted systematic evolution of ligands by exponential enrichment (E-SELEX) is developed to generate a high-quality aptamer (CCE-10F) that recognizes and binds to CRC-derived sEVs. Via an in-depth investigation, it is confirmed that this novel aptamer possesses high affinity (Kd = 3.41 nm) for CRC-derived sEVs and exhibits a wide linear range (2.0 × 104 -1.0 × 106 particles µL-1 ) with a limit of detection (LOD) of 1.0 × 103 particles µL-1 . Furthermore, the aptamer discriminates CRC cell-derived sEVs from those derived from normal colon cell, human serum, and other cancer cells, showing high specificity for CRC cell-derived sEVs and significantly suppresses the critical processes of metastasis, including cellular migration, invasion, and angiogenesis, which are originally induced by sEVs themselves. These findings are highly encouraging for the potential use of the aptamer in sEV-based diagnostic and therapeutic applications.
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Affiliation(s)
- Byung Seok Cha
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Young Jun Jang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Eun Sung Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Do Yeon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ji Su Woo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jinseo Son
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jiye Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jinjoo Han
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seokhwan Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
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Lupu L, Kleinekofort W, Morgner N. Epitope characterization of proteins and aptamers with mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:359-369. [PMID: 37957929 DOI: 10.1177/14690667231208530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The way in which professor Michael Przybylski has combined the spirit of research with entrepreneurship has set an example for any and all scientists. He has made significant achievements in the fields of mass spectrometry, biochemistry and medicine, and has initiated important technological developments in the area of protein analysis. Between 2016 and 2023 professor Przybylski's scientific focus shifted on protein interactions with emphasis on aptamer-protein and antibody-protein analysis. This review focuses on professor Przybylski's achievements in the last few years highlighting his impact on the scientific community, on his students and colleagues.
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Affiliation(s)
- Loredana Lupu
- AffyMSLifeChem Centre for Analytical Biochemistry and Biomedical Mass Spectrometry, Rüsselsheim am Main, Germany
| | | | - Nina Morgner
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt am Main, Frankfurt Am Main, Germany
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Van den Avont A, Sharma-Walia N. Anti-nucleolin aptamer AS1411: an advancing therapeutic. Front Mol Biosci 2023; 10:1217769. [PMID: 37808518 PMCID: PMC10551449 DOI: 10.3389/fmolb.2023.1217769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/01/2023] [Indexed: 10/10/2023] Open
Abstract
Targeted therapy is highly desirable, as it allows for selective cytotoxicity on diseased cells without off-target side effects. Nucleolin is a remarkable target for cancer therapy given its high abundance, selective presence on the plasma membrane, and multifaceted influence on the initiation and progression of cancer. Nucleolin is a protein overexpressed on the cell membrane in many tumors and serves as a binding protein for several ligands implicated in angiogenesis and tumorigenesis. Nucleolin is present in the cytoplasm, nucleoplasm, and nucleolus and is used by selected pathogens for cell entry. AS1411 is a guanosine-rich oligonucleotide aptamer that binds nucleolin and is internalized in the tumor cells. AS1411 is well tolerated at therapeutic doses and localizes to tumor cells overexpressing nucleolin. AS1411 has a good safety profile with efficacy in relapsed acute myeloid leukemia and renal cell carcinoma producing mild or moderate side effects. The promising potential of AS1411 is its ability to be conjugated to drugs and nanoparticles. When a drug is bound to AS1411, the drug will localize to tumor cells leading to targeted therapy with fewer systemic side effects than traditional practices. AS1411 can also be bound to nanoparticles capable of detecting nucleolin at concentrations far lower than lab techniques used today for cancer diagnosis. AS1411 has a promising potential to change cancer diagnoses and treatment.
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Affiliation(s)
| | - Neelam Sharma-Walia
- Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
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Economou A, Kokkinos C, Bousiakou L, Hianik T. Paper-Based Aptasensors: Working Principles, Detection Modes, and Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:7786. [PMID: 37765843 PMCID: PMC10536119 DOI: 10.3390/s23187786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Aptamers are short oligonucleotides designed to possess high binding affinity towards specific target compounds (ions, molecules, or cells). Due to their function and unique advantages, aptamers are considered viable alternatives to antibodies as biorecognition elements in bioassays and biosensors. On the other hand, paper-based devices (PADs) have emerged as a promising and powerful technology for the fabrication of low-cost analytical tools, mainly intended for on-site and point-of-care applications. The present work aims to provide a comprehensive overview of paper-based aptasensors. The review describes the fabrication methods and working principles of paper-based devices, the properties of aptamers as bioreceptors, the different modes of detection used in conjunction with aptasensing PADs, and representative applications for the detection of ions, small molecules, proteins, and cells. The future challenges and prospects of these devices are also discussed.
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Affiliation(s)
- Anastasios Economou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Christos Kokkinos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Leda Bousiakou
- IMD Laboratories Co., R&D Section, Lefkippos Technology Park, National Centre for Scientific Research (NCSR) Demokritos, Agia Paraskevi, P.O. Box 60037, 15130 Athens, Greece;
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 84248 Bratislava, Slovakia;
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48
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Liu Y, Potts JL, Bloch D, Nian K, McCormick CA, Fanari O, Rouhanifard SH. Paired Capture and FISH Detection of Individual Virions Enable Cell-Free Determination of Infectious Titers. ACS Sens 2023; 8:2563-2571. [PMID: 37368999 PMCID: PMC10621038 DOI: 10.1021/acssensors.3c00239] [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: 02/08/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Early detection of viruses can prevent the uncontrolled spread of viral infections. Determination of viral infectivity is also critical for determining the dosage of gene therapies, including vector-based vaccines, CAR T-cell therapies, and CRISPR therapeutics. In both cases, for viral pathogens and viral vector delivery vehicles, fast and accurate measurement of infectious titers is desirable. The most common methods for virus detection are antigen-based (rapid but not sensitive) and polymerase chain reaction (PCR)-based (sensitive but not rapid). Current viral titration methods heavily rely on cultured cells, which introduces variability within labs and between labs. Thus, it is highly desirable to directly determine the infectious titer without using cells. Here, we report the development of a direct, fast, and sensitive assay for virus detection (dubbed rapid capture fluorescence in situ hybridization (FISH) or rapture FISH) and cell-free determination of infectious titers. Importantly, we demonstrate that the virions captured are "infectious," thus serving as a more consistent proxy of infectious titers. This assay is unique because it first captures viruses bearing an intact coat protein using an aptamer and then detects genomes directly in individual virions using fluorescence in situ hybridization (FISH); thus, it is selective for infectious particles (i.e., positive for coat proteins and positive for genomes).
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Affiliation(s)
- Yifang Liu
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jacob L. Potts
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dylan Bloch
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Keqing Nian
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Caroline A. McCormick
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Oleksandra Fanari
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sara H. Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, 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
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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Mishra Y, Chattaraj A, Mishra V, Ranjan A, Tambuwala MM. Aptamers Versus Vascular Endothelial Growth Factor (VEGF): A New Battle against Ovarian Cancer. Pharmaceuticals (Basel) 2023; 16:849. [PMID: 37375796 DOI: 10.3390/ph16060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/28/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer is one of the diseases that causes a high mortality as it involves unregulated and abnormal cell growth proliferation that can manifest in any body region. One of the typical ovarian cancer symptoms is damage to the female reproductive system. The death rate can be reduced through early detection of the ovarian cancer. Promising probes that can detect ovarian cancer are suitable aptamers. Aptamers, i.e., so-called chemical antibodies, have a strong affinity for the target biomarker and can typically be identified starting from a random library of oligonucleotides. Compared with other probes, ovarian cancer targeting using aptamers has demonstrated superior detection effectiveness. Various aptamers have been selected to detect the ovarian tumor biomarker, vascular endothelial growth factor (VEGF). The present review highlights the development of particular aptamers that target VEGF and detect ovarian cancer at its earliest stages. The therapeutic efficacy of aptamers in ovarian cancer treatment is also discussed.
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Affiliation(s)
- Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Aditi Chattaraj
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Abhigyan Ranjan
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, UK
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