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Gandotra R, Wu HB, Kuo FC, Lee MS, Lee GB. Advancing the Diagnosis of Periprosthetic Joint Infections: Integrated Microfluidic Platform for Alpha-Defensins-Specific Aptamer Selection and Its Analytical Applications. ACS Sens 2024; 9:1775-1784. [PMID: 38591344 DOI: 10.1021/acssensors.3c02034] [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: 04/10/2024]
Abstract
Periprosthetic joint infections (PJIs) pose a significant challenge in orthopedic surgery, particularly total joint arthroplasty (TJA), due to the potential for implant failure and increased patient morbidity. Early and accurate detection of PJIs is crucial for timely intervention and better patient prognosis. Herein, we successfully screened a high-affinity aptamer targeting alpha-defensin complex human neutrophil protein 1-3 (HNP 1-3; potential PJI biomarkers in synovial fluid [SF]) for the first time using systematic evolution of ligands by exponential enrichment (SELEX) on an integrated microfluidic platform. The compact microfluidic device enabled efficient screening, with each round completed within <2 h, comprising five rounds of positive selection, two rounds of negative selection, and one round of competitive selection. A novel one-aptamer-one-antibody assay was further developed from the optimal aptamer screened, and it could accurately quantify HNP 1-3 in SF within 3 h with only ∼50 μL of SF. The assay demonstrated strong binding affinity and specificity for the target protein in SF. Thirteen PJI SF samples were accurately diagnosed and the assay was accurate over a wide dynamic range (0.32-100 mg/L). This study has showcased a rapid and accurate diagnostic tool for PJI detection, which should see widespread use in the clinic, holding promise for potential analytical applications in orthopedic surgery and improving patient care.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung-Bin Wu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung 83301, Taiwan
| | - Mel S Lee
- Department of Orthopaedic Surgery, Paochien Hospital, Pingtung 90064, Taiwan
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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Roshan U, Mudugamuwa A, Cha H, Hettiarachchi S, Zhang J, Nguyen NT. Actuation for flexible and stretchable microdevices. LAB ON A CHIP 2024; 24:2146-2175. [PMID: 38507292 DOI: 10.1039/d3lc01086d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Flexible and stretchable microdevices incorporate highly deformable structures, facilitating precise functionality at the micro- and millimetre scale. Flexible microdevices have showcased extensive utility in the fields of biomedicine, microfluidics, and soft robotics. Actuation plays a critical role in transforming energy between different forms, ensuring the effective operation of devices. However, when it comes to actuating flexible microdevices at the small millimetre or even microscale, translating actuation mechanisms from conventional rigid large-scale devices is not straightforward. The recent development of actuation mechanisms leverages the benefits of device flexibility, particularly in transforming conventional actuation concepts into more efficient approaches for flexible devices. Despite many reviews on soft robotics, flexible electronics, and flexible microfluidics, a specific and systematic review of the actuation mechanisms for flexible and stretchable microdevices is still lacking. Therefore, the present review aims to address this gap by providing a comprehensive overview of state-of-the-art actuation mechanisms for flexible and stretchable microdevices. We elaborate on the different actuation mechanisms based on fluid pressure, electric, magnetic, mechanical, and chemical sources, thoroughly examining and comparing the structure designs, characteristics, performance, advantages, and drawbacks of these diverse actuation mechanisms. Furthermore, the review explores the pivotal role of materials and fabrication techniques in the development of flexible and stretchable microdevices. Finally, we summarise the applications of these devices in biomedicine and soft robotics and provide perspectives on current and future research.
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Affiliation(s)
- Uditha Roshan
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
| | - Amith Mudugamuwa
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
| | - Haotian Cha
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
| | - Samith Hettiarachchi
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
| | - Jun Zhang
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
- School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane, QLD 4111, Australia.
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Chang JL, Huang CJ, Tsai YC, Chiang NJ, Huang YS, Hung SC, Shan YS, Lee GB. An integrated microfluidic system for automatic detection of cholangiocarcinoma cells from bile. LAB ON A CHIP 2024; 24:375-382. [PMID: 38126571 DOI: 10.1039/d3lc00862b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Cholangiocarcinoma (CCA) is an aggressive cancer that originates from the epithelial cells lining the bile ducts. Due to its location deep within the body and nonspecific symptoms in the early stages, it is often diagnosed at the advanced stage, thus leading to worse prognosis. Circulating tumor cells within liquid biopsies (i.e. blood) have been considered as promising biomarkers for CCA diagnosis, though current methods for profiling them are not satisfactory in terms of sensitivity and specificity. Herein we developed a new cancer cell probing and immuno-tracking assay known as "CAPTURE", which was performed on an integrated microfluidic system (IMS) to automate CCA diagnosis from bile with a sample amount of only 1 mL. The assay utilized magnetic beads surface-coated with two affinity reagents, a nucleic acid aptamer (HN16) and a glycosaminoglycan (SCH 45-mix), for capturing cancer cells in bile; the "gold standard" anti-epithelial cell adhesion molecule was used as a comparison. In a single-blind test of 54 CCA-positive (+) and 102 CCA-negative (-) clinical samples, sensitivities and specificities of 96 and 80%, respectively, were documented with the CAPTURE assay on-bench. An IMS composed of a centrifugal module for sample pretreatment and a CAPTURE module for cell capture and staining was integrated with a new "vertical integration module" for detecting cancer cells from bile without human intervention. Furthermore, a novel micro-tier structure within the centrifugal module was designed to block passage of gallbladder stones with diameters >1 mm, thereby preventing their interference during the subsequent CAPTURE assay. Improved sensitivity and specificity (100 & 83%, respectively) by using three affinity reagents were achieved on the IMS when using 26 clinical bile samples, confirming its clinical bio-applicability for CCA diagnosis. This approach could be therefore used for early-stage CCA diagnostics, ideally enabling effective treatment, as well as reducing potential for relapse.
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Affiliation(s)
- Jui-Lin Chang
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
| | - Chien-Jui Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Cheng Tsai
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Nai-Jung Chiang
- Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Yu-Shan Huang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gwo-Bin Lee
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu, Taiwan
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Gandotra R, Kuo FC, Lee MS, Lee GB. A paper-based aptamer-sandwich assay for detection of HNP 1 as a biomarker for periprosthetic joint infections on an integrated microfluidic platform. Anal Chim Acta 2023; 1281:341879. [PMID: 38783735 DOI: 10.1016/j.aca.2023.341879] [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: 09/25/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 05/25/2024]
Abstract
BACKGROUND Total joint arthroplasty (TJA) has significantly improved the quality of life for millions suffering from end-stage arthritis. However, periprosthetic joint infections (PJI) remain a serious complication, necessitating extensive interventions and prolonged antimicrobial treatments. The aging population is expected to lead to a rise in TJA cases, subsequently increasing the incidence of PJI, particularly in the elderly who face higher mortality rates. Current diagnostic methods for suspected PJI, such as radiographs and biochemical markers like CRP and ESR, exhibit limited sensitivity. Therefore, there is a critical need for a specific synovial fluid biomarker assay to enhance PJI diagnosis using specific SF-based assay. RESULTS This study introduces a novel microfluidic chip with a paper-based aptamer-sandwich assay for the quantitative detection of HNP 1, a crucial PJI biomarker, in synovial fluid. The assay leverages the advantages of aptamers over antibodies, demonstrating high selectivity and affinity for target molecules. The integration of a nitrocellulose (NC) membrane onto the microfluidic platform represents a significant advancement, reducing background signals and simplifying the assay procedure without intricate procedure and pre-treatment. The NC membrane-based microfluidic device offers rapid, cost-effective, and highly sensitive detection of HNP 1, with a limit of detection of 0.5 mg L-1. The microfluidic device demonstrates exceptional performance, detecting up to four clinical samples in approximately 42 min on a single chip with 100 % accuracy, as confirmed by analysis of 12 clinical samples and comparison with "gold-standard". Moreover, the assay exhibits a wide dynamic range of 0.5-100 mg L-1, underscoring its potential as a powerful tool for PJI diagnosis in clinical settings. SIGNIFICANCE This work introduces a paper-based microfluidic system tailored for rapid HNP 1 detection using synovial fluid near joint region (and not serum via blood) for better diagnosis. The innovative paper-based aptamer-sandwich assay yields results within 42-min. Significantly, it boasts a wide dynamic range, detecting levels from an impressive 0.5 mg L-1, crucial in the 2.6 mg L-1 threshold region. This heightened sensitivity and expansive detection capability establish our assay as a leader in PJI diagnostics, promising unmatched precision and efficiency in clinical applications.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Mel S Lee
- Department of Orthopedic Surgery, Paochien Hospital, Pintung, Taiwan.
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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Gandotra R, Chen TW, Kuo FC, Lee MS, Lee GB. An aptamer-based sandwich assay for detection of alpha-defensin human neutrophil protein 1 on a microfluidic platform. Biosens Bioelectron 2023; 229:115120. [PMID: 36963324 DOI: 10.1016/j.bios.2023.115120] [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: 10/07/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The diagnosis of periprosthetic joint infection (PJI) remains a labor-intensive and challenging issue, with life-threatening complications associated with misdiagnoses. Superior diagnostic approaches are therefore urgently needed, and synovial biomarkers are gaining substantial attention in this capacity. A new aptamer-based sandwich assay was developed where the aptamer probes specific to one such biomarker, alpha-defensin human neutrophil protein 1 (HNP 1), was integrated herein into a new microfluidic platform. The magnetic beads coated with the primary aptamer probe were able to bind the target protein with high affinity and high specificity in synovial fluid and a fluorescent-labelled secondary aptamer were further used to quantify HNP 1 in a sandwich approach. Up to four clinical samples with low volume (∼50 μL each) in a much faster assay including detection within <60 min with 100% accuracy (with totally 13 clinical samples without the need of sample pretreatment) through the use of the aptamer-based sandwich assay were automatically detected on a single chip. The wide dynamic range of this compact device, 0.5-100 mg/L, highlights its utility for future PJI diagnostics in the clinic.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - To-Wen Chen
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Mel S Lee
- Department of Orthopedic Surgery, Paochien Hospital, Pintung, Taiwan.
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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CD44 and CD133 aptamer directed nanocarriers for cancer stem cells targeting. Eur Polym J 2023. [DOI: 10.1016/j.eurpolymj.2022.111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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El-Husseini DM, Sayour AE, Melzer F, Mohamed MF, Neubauer H, Tammam RH. Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology. Int J Mol Sci 2022; 23:ijms23116131. [PMID: 35682807 PMCID: PMC9180945 DOI: 10.3390/ijms23116131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (KD) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.
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Affiliation(s)
- Dalia M. El-Husseini
- Biotechnology Department, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Ashraf E. Sayour
- Molecular Biomimetics Research Group, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt;
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Magda F. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
| | - Reham H. Tammam
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
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Research progress of whole-cell-SELEX selection and the application of cell-targeting aptamer. Mol Biol Rep 2022; 49:7979-7993. [PMID: 35274201 DOI: 10.1007/s11033-022-07317-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aptamers refer to the artificially synthesized nucleic acid sequences (DNA/RNA) that can bind to a wide range of targets with high affinity and specificity, which are generally generated from systematic evolution of ligands by exponential enrichment (SELEX). As a novel method of aptamers screening, whole-cell-SELEX (WC-SELEX) has gained more and more attention in many fields such as biomedicine, analytical chemistry, and molecular diagnostics due to its ability to screen multiple potential aptamers without knowing the detailed structural information of target molecules. METHODS AND RESULTS In recent years, with the deepening of research on application of aptamers, the traditional WC-SELEX cannot meet the practical application because of long experimental period, complicated operation process and low specificity, etc. Therefore, the development of more efficient methods for screening aptamer is always on the road. This paper summarizes the current research status of WC-SELEX for bacteria, parasites and animal cells, and reviews the latest advances of WC-SELEX techniques that are dependent on novel instruments, materials and microelectronics, including fluorescence-activated cell sorting-assisted SELEX, three-dimensional assisted WC-SELEX, and microfluidic chip system-assisted WC-SELEX. In addition, the application of aptamers targeting cells was discussed. CONCLUSION Taken together, this review is aimed at providing a reference for WC-SELEX selection and application of aptamer targeting cells.
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Xiao X, Li H, Zhao L, Zhang Y, Liu Z. Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications. Biomed Pharmacother 2021; 143:112232. [PMID: 34649356 DOI: 10.1016/j.biopha.2021.112232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/04/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.
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Affiliation(s)
- Xueran Xiao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hui Li
- Department of Urology, Peking University International Hospital, Beijing 102206, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yanfen Zhang
- Technology Transfer Center, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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Kim DM, Go MJ, Lee J, Na D, Yoo SM. Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies. Molecules 2021; 26:5187. [PMID: 34500620 PMCID: PMC8434002 DOI: 10.3390/molecules26175187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.
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Affiliation(s)
- Dong-Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Myeong-June Go
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Seung-Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
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Aptamers Against Live Targets: Is In Vivo SELEX Finally Coming to the Edge? MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:192-204. [PMID: 32585627 PMCID: PMC7321788 DOI: 10.1016/j.omtn.2020.05.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/18/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
Abstract
Targeted therapeutics underwent a revolution with the entry of monoclonal antibodies in the medical toolkit. Oligonucleotide aptamers form another family of target agents that have been lagging behind in reaching the clinical arena in spite of their potential clinical translation. Some of the reasons for this might be related to the challenge in identifying aptamers with optimal in vivo specificity, and the nature of their pharmacokinetics. Aptamers usually show exquisite specificity, but they are also molecules that display dynamic structures subject to changing environments. Temperature, ion atmosphere, pH, and other variables are factors that could determine the affinity and specificity of aptamers. Thus, it is important to tune the aptamer selection process to the conditions in which you want your final aptamer to function; ideally, for in vivo applications, aptamers should be selected in an in vivo-like system or, ultimately, in a whole in vivo organism. In this review we recapitulate the implementations in systematic evolution of ligands by exponential enrichment (SELEX) to obtain aptamers with the best in vivo activity.
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Zhong Y, Zhao J, Li J, Liao X, Chen F. Advances of aptamers screened by Cell-SELEX in selection procedure, cancer diagnostics and therapeutics. Anal Biochem 2020; 598:113620. [PMID: 32087127 DOI: 10.1016/j.ab.2020.113620] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/23/2022]
Abstract
Aptamers are a class of short artificial single-stranded oligo(deoxy) nucleotides that can bind to different targets, which generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Due to excellent selectivity and high affinity to targets, aptamers hold considerable potential as molecular probe in diverse applications ranging from ensuring food safety, monitoring environment, disease diagnosis to therapy. This review highlights recent development and challenges about aptamers screened by Cell-SELEX, and its application about cancer diagnostics and therapeutics. Advances about some operation methods such as seperation method and culture method in aptamers selection procedure were summarized in this paper. Some common challenges and technological difficulties such as nonspecific binding and biostability were discussed. Up to now, the recent endeavors about cancer diagnostic and therapeutic applications of aptamers are summarized and expatiated. Most of aptamers screened by Cell-SELEX took tumor cells as target cells, and such aptamers have been assembled to various aptasensor for cancer diagnosis. Aptamers conjugated various drugs or nanomaterials are functioned for cancer target therapy to improve drugs delivery efficiency and reduce side effects. Furthermore, the duplexed aptamer is discussed to be applied for cancer cells detection and some conflicts of theories about duplexed aptamer designs are analyzed.
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Affiliation(s)
- Yi Zhong
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China; National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiayao Zhao
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China; National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiazhao Li
- Qionglai maternal&Child health care hospital, Chengdu, 611530, Sichuan, China
| | - Xin Liao
- School of laboratory medical and Life science, Wenzhou Medical University, Wenzhou, 325000, Fujian, China
| | - Fengling Chen
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Gopinathan P, Sinha A, Chung YD, Shiesh SC, Lee GB. Optimization of an enzyme linked DNA aptamer assay for cardiac troponin I detection: synchronous multiple sample analysis on an integrated microfluidic platform. Analyst 2019; 144:4943-4951. [PMID: 31317135 DOI: 10.1039/c9an00779b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this study, an enzyme linked DNA aptamer based assay was optimized for human cardiac troponin I (cTnI) detection which is a prominent biomarker for acute myocardial infarction (AMI), on an integrated microfluidic platform. This platform allowed for the multiplex detection of six samples (5 μL per sample), and only 30 min were required for detection. First, cTnI-specific aptamers were surface-coated on magnetic beads. Bead-captured proteins were allowed to bind to a primary cTnI antibody and then to a secondary antibody labelled with horseradish peroxidase. Finally, chemiluminescence intensities were detected for quantification of cTnI. Purified proteins, serum from AMI patients and unknown serum samples were used to test the efficacy of the on-chip system. The limit of detection was measured to be only 12 ng L-1, and off-target effects from other proteins were minimal. This sensitive, cTnI-specific aptamer-based assay could consequently be used for reliable diagnosis of AMI.
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Affiliation(s)
- Priya Gopinathan
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
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Bing T, Zhang N, Shangguan D. Cell-SELEX, an Effective Way to the Discovery of Biomarkers and Unexpected Molecular Events. ACTA ACUST UNITED AC 2019; 3:e1900193. [PMID: 32648677 DOI: 10.1002/adbi.201900193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Cell-SELEX can not only generate aptamers for specific cell isolation/detection, diagnosis, and therapy, but also lead to the discovery of biomarkers and unexpected molecular events. However, most cell-SELEX research is concentrated on aptamer generation and applications. In this progress report, recent research progress with cell-SELEX in terms of the discovery of biomarkers and unexpected molecular events is highlighted. In particular, the key technical challenges for cell-SELEX-based biomarker discovery, namely, the methods for identification and validation of target proteins of aptamers, are discussed in detail. Finally, the prospects of the applications of cell-SELEX in this field now and in the near future are described. It is expected that this report will attract attention to the benefit of cell-SELEX and provide a practical reference for biomedical researchers.
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Affiliation(s)
- Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Yan J, Xiong H, Cai S, Wen N, He Q, Liu Y, Peng D, Liu Z. Advances in aptamer screening technologies. Talanta 2019; 200:124-144. [DOI: 10.1016/j.talanta.2019.03.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/20/2019] [Accepted: 03/02/2019] [Indexed: 02/07/2023]
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Sinha A, Gopinathan P, Chung YD, Shiesh SC, Lee GB. Simultaneous detection of multiple NT-proBNP clinical samples utilizing an aptamer-based sandwich assay on an integrated microfluidic system. LAB ON A CHIP 2019; 19:1676-1685. [PMID: 30942226 DOI: 10.1039/c9lc00115h] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although cardiovascular diseases such as heart failure (HF) affect 30 million people globally, the early detection of HF has, until recently, been difficult and prone to misdiagnoses. Monitoring the circulatory levels of a relatively new biomarker, the N-terminal prohormone of a B-type natriuretic peptide, could be used for early risk evaluation of HF. Therefore, we developed a pneumatically-driven, automatic integrated microfluidic platform equipped with micromixers, micropumps, and microvalves for the simultaneous detection of NT-proBNP in up to six clinical samples within 25 min by using a novel aptamer-based sandwich assay, and the limit of detection was only 1.53 pg mL-1; given that the chip is 64% more compact than those developed in our prior works and requires only 5 μL of sample input, it may serve as a promising tool for early diagnosis of HF.
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Affiliation(s)
- Anirban Sinha
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan.
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Maimaitiyiming Y, Hong DF, Yang C, Naranmandura H. Novel insights into the role of aptamers in the fight against cancer. J Cancer Res Clin Oncol 2019; 145:797-810. [PMID: 30830295 DOI: 10.1007/s00432-019-02882-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Aptamers are a class of single-stranded nucleic acid (DNA or RNA) oligonucleotides that are screened in vitro by a technique called systematic evolution of ligands by exponential enrichment (SELEX). They have stable three-dimensional structures that can bind to various targets with high affinity and specificity. Due to distinct properties such as easy synthesis, high stability, small size, low toxicity and immunogenicity, they have been largely studied as anticancer agents/tools. Consequently, aptamers are starting to play important roles in disease prevention, diagnosis and therapy. This review focuses on studies that evaluated the effect of aptamers on various aspects of cancer therapy. It also provides novel and unique insights into the role of aptamers on the fight against cancer. METHODS We reviewed literatures about the role of aptamers against cancer from PUBMED databases in this article. RESULTS Here, we summarized the role of aptamers on the fight against cancer in a unique point of view. Meanwhile, we presented novel ideas such as aptamer-pool-drug conjugates for the treatment of refractory cancers. CONCLUSIONS Aptamers and antibodies should form a "coalition" against cancers to maximize their advantages and minimize disadvantages.
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Affiliation(s)
- Yasen Maimaitiyiming
- Department of Pharmacology, School of Medicine, Zhejiang University, Hangzhou, China
| | - De Fei Hong
- The Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chang Yang
- Department of Pharmacology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Naranmandura
- Department of Pharmacology, School of Medicine, Zhejiang University, Hangzhou, China. .,Department of Toxicology, School of Medicine and Public Health, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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Sinha A, Gopinathan P, Chung YD, Lin HY, Li KH, Ma HP, Huang PC, Shiesh SC, Lee GB. An integrated microfluidic platform to perform uninterrupted SELEX cycles to screen affinity reagents specific to cardiovascular biomarkers. Biosens Bioelectron 2018; 122:104-112. [PMID: 30245322 DOI: 10.1016/j.bios.2018.09.040] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 12/19/2022]
Abstract
As cardiovascular diseases (CVD) are responsible for millions of deaths annually, there is a need for rapid and sensitive diagnosis of CVD at earlier stages. Aptamers generated by systematic evolution of ligands by exponential enrichment (SELEX) processes have been shown to be superior to conventional antibody-based cardiac biomarker detection. However, SELEX is a complicated, lengthy procedure requiring multiple rounds of extraction/amplification and well-trained personnel. To circumvent such issue, we designed an automated, miniaturized SELEX platform for the screening of aptamers towards three protein biomarkers associated with CVDs: N-terminal pro-peptide of B-type natriuretic peptide, human cardiac troponin I, and fibrinogen. The developed microfluidic platform was equipped with microfluidic devices capable of sample transport and mixing along with an on-chip nucleic acid amplification module such that the entire screening process (5 rounds of selection in 8 h.) could be performed consecutively on a single chip while consuming only 35 µL of reagents in each cycle. This system may therefore serve as a promising, sensitive, cost-effective platform for the selection of aptamers specific for CVD biomarkers.
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Affiliation(s)
- Anirban Sinha
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Priya Gopinathan
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Da Chung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hsin-Ying Lin
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Kuang-Hsien Li
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsi-Pin Ma
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Po-Chiun Huang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Shu-Chu Shiesh
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Gwo-Bin Lee
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
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Kaur H. Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj 2018; 1862:2323-2329. [PMID: 30059712 DOI: 10.1016/j.bbagen.2018.07.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND SELEX technique is employed to select aptamers against wide range of targets. The in vitro method of aptamer selection using live cells as the target is referred as cell-SELEX. SCOPE OF THE REVIEW The review provides a comprehensive description on the development of aptamers through various cell-SELEX methods and list of aptamers identified through this method. In addition, it pinpoints the advantages and limitations of the cell-SELEX process and its variants. MAJOR CONCLUSIONS The use of aptamers as therapeutic and diagnostic agents is rapidly evolving, selection techniques such as Cell-SELEX could be beneficial in identifying aptamers when the target is in its native conformation and without prior information of the cognate target, thereby bringing the aptamer development one step closer to the clinic. GENERAL SIGNIFICANCE The information in this review can serve as a database for the design and development of futuristic oligonucleotide based diagnostics and therapeutics work.
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Catuogno S, Esposito CL. Aptamer Cell-Based Selection: Overview and Advances. Biomedicines 2017; 5:biomedicines5030049. [PMID: 28805744 PMCID: PMC5618307 DOI: 10.3390/biomedicines5030049] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 02/07/2023] Open
Abstract
Aptamers are high affinity single-stranded DNA/RNA molecules, produced by a combinatorial procedure named SELEX (Systematic Evolution of Ligands by Exponential enrichment), that are emerging as promising diagnostic and therapeutic tools. Among selection strategies, procedures using living cells as complex targets (referred as "cell-SELEX") have been developed as an effective mean to generate aptamers for heavily modified cell surface proteins, assuring the binding of the target in its native conformation. Here we give an up-to-date overview on cell-SELEX technology, discussing the most recent advances with a particular focus on cancer cell targeting. Examples of the different protocol applications and post-SELEX strategies will be briefly outlined.
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Affiliation(s)
- Silvia Catuogno
- Istituto di Endocrinologia ed Oncologia Sperimentale "G. Salvatore", CNR, Naples 80100, Italy.
| | - Carla Lucia Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale "G. Salvatore", CNR, Naples 80100, Italy.
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