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Ngo LT, Chaudhari P, Wang WK, Tseng YT, Kuo PL, Huang CJ, Chiang CY, Chau LK, Huang TT. Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay. ACS Sens 2024; 9:4207-4215. [PMID: 39088458 DOI: 10.1021/acssensors.4c01194] [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: 08/03/2024]
Abstract
β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.
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Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pallavi Chaudhari
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Wei-Kai Wang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, College of Medicine, National Cheng Kung University Hospital, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, 1 Yida Rd., Yanchao District, Kaohsiung City 82445, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, 300 Zhongda Rd., Zhongli District, Taoyuan City 320, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung Pei Rd., Chung-Li City 32023, Taiwan
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
- Center for Nano Bio-Detection, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Tze-Ta Huang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Stomatology, College of Medicine and Hospital, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
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Tariq Z, Qadeer MI, Anjum I, Hano C, Anjum S. Thalassemia and Nanotheragnostics: Advanced Approaches for Diagnosis and Treatment. BIOSENSORS 2023; 13:bios13040450. [PMID: 37185525 PMCID: PMC10136341 DOI: 10.3390/bios13040450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 05/17/2023]
Abstract
Thalassemia is a monogenic autosomal recessive disorder caused by mutations, which lead to abnormal or reduced production of hemoglobin. Ineffective erythropoiesis, hemolysis, hepcidin suppression, and iron overload are common manifestations that vary according to genotypes and dictate, which diagnosis and therapeutic modalities, including transfusion therapy, iron chelation therapy, HbF induction, gene therapy, and editing, are performed. These conventional therapeutic methods have proven to be effective, yet have several disadvantages, specifically iron toxicity, associated with them; therefore, there are demands for advanced therapeutic methods. Nanotechnology-based applications, such as the use of nanoparticles and nanomedicines for theragnostic purposes have emerged that are simple, convenient, and cost-effective methods. The therapeutic potential of various nanoparticles has been explored by developing artificial hemoglobin, nano-based iron chelating agents, and nanocarriers for globin gene editing by CRISPR/Cas9. Au, Ag, carbon, graphene, silicon, porous nanoparticles, dendrimers, hydrogels, quantum dots, etc., have been used in electrochemical biosensors development for diagnosis of thalassemia, quantification of hemoglobin in these patients, and analysis of conventional iron chelating agents. This review summarizes the potential of nanotechnology in the development of various theragnostic approaches to determine thalassemia-causing gene mutations using various nano-based biosensors along with the employment of efficacious nano-based therapeutic procedures, in contrast to conventional therapies.
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Affiliation(s)
- Zahra Tariq
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
| | | | - Iram Anjum
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
| | - Christophe Hano
- Department of Chemical Biology, Eure & Loir Campus, University of Orleans, 28000 Chartres, France
| | - Sumaira Anjum
- Department of Biotechnology, Kinnaird College for Women, 92-Jail Road, Lahore 54000, Pakistan
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Burck N, Gilboa T, Gadi A, Patkin Nehrer M, Schneider RJ, Meller A. Nanopore Identification of Single Nucleotide Mutations in Circulating Tumor DNA by Multiplexed Ligation. Clin Chem 2021; 67:753-762. [PMID: 33496315 DOI: 10.1093/clinchem/hvaa328] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Circulating tumor DNAs (ctDNAs) are highly promising cancer biomarkers, potentially applicable for noninvasive liquid biopsy and disease monitoring. However, to date, sequencing of ctDNAs has proven to be challenging primarily due to small sample size and high background of fragmented cell-free DNAs (cfDNAs) derived from normal cells in the circulation, specifically in early stage cancer. METHODS Solid-state nanopores (ssNPs) have recently emerged as a highly efficient tool for single-DNA sensing and analysis. Herein, we present a rapid nanopore genotyping strategy to enable an amplification-free identification and classification of ctDNA mutations. A biochemical ligation detection assay was used for the creation of specific fluorescently-labelled short DNA reporter molecules. Color conjugation with multiple fluorophores enabled a unique multi-color signature for different mutations, offering multiplexing potency. Single-molecule readout of the fluorescent labels was carried out by electro-optical sensing via solid-state nanopores drilled in titanium oxide membranes. RESULTS As proof of concept, we utilized our method to detect the presence of low-quantity ERBB2 F310S and PIK3Ca H1047R breast cancer mutations from both plasmids and xenograft mice blood samples. We demonstrated an ability to distinguish between a wild type and a mutated sample, and between the different mutations in the same sample. CONCLUSIONS Our method can potentially enable rapid and low cost ctDNA analysis that completely circumvents PCR amplification and library preparation. This approach will thus meet a currently unmet demand in terms of sensitivity, multiplexing and cost, opening new avenues for early diagnosis of cancer.
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Affiliation(s)
- Nitza Burck
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel
| | - Tal Gilboa
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Abhilash Gadi
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | | | | | - Amit Meller
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel.,Russell Berrie Nanotechnology Institute, Technion- IIT, Haifa, Israel
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Shlyapnikov YM, Malakhova EA, Shlyapnikova EA. Rapid Amplification-Free Microarray-Based Ultrasensitive Detection of DNA. Anal Chem 2019; 91:11209-11214. [DOI: 10.1021/acs.analchem.9b02149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuri M. Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
| | - Ekaterina A. Malakhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
| | - Elena A. Shlyapnikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow
Region, 142290, Russia
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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Yan L, Deng Z, Shi H, Xie B, Gao L. A method for SNP detection using MoS 2@AuNPs and SYBR Green I in combination with enzyme digestion. NEW J CHEM 2019. [DOI: 10.1039/c9nj04319e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases.
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Affiliation(s)
- Lirong Yan
- Department of Gerontology
- Affiliated Hospital of Jiangsu University
- Zhenjiang 212001
- China
| | - Zebin Deng
- Institute of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Haixia Shi
- P. E. Department of Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Bing Xie
- Department of Obstetrics and Gynecology
- The Fourth People's Hospital of Zhenjiang
- Zhenjiang
- P. R. China
| | - Li Gao
- Institute of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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Heidari Sharafdarkolaee S, Motovali-Bashi M, Gill P. The sensitive detection of IVSII-1(G˃A) mutation in beta globin gene using a Nano-based ligation genotyping system. Gene 2018; 674:98-103. [PMID: 29913238 DOI: 10.1016/j.gene.2018.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
Beta-thalassemia (β-thalassemia) is a globally genetic diseases, and is most prevalent in the Middle East, particularly in Iran. Carrier detection and prenatal diagnosis are the best ways to managing it, and to prevent new community cases from emerging. We report on a simple method for rapid detection of the worst β-thalassemia point mutation in Iran (IVS-II-1 G>A), using a nano-based ligation assay, this was performed using probes with labeled magnetic nanoparticles and quantum dots. After optimizing the technique, 50 DNA samples were genotyped with this method. We found a frequency of 72% for IVSII-1 (G˃A) mutation (42% heterozygote, and 30% mutant homozygote) with a highly sensitive nano-based ligation genotyping system, offering excellent sensitivity and specificity for point mutation detection; it has been demonstrated to be inaccurate, sensitive, cost-effective, and rapid technique for single nucleotide polymorphism (SNP) genotyping.
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Affiliation(s)
| | - Majid Motovali-Bashi
- Genetics Division, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.
| | - Pooria Gill
- Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Sari, Iran; Nanomedicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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