Isolation of RNA Aptamers Targeting HER-2-overexpressing Breast Cancer Cells Using Cell-SELEX

Kang, Hye Suk; Huh, Yong Min; Kim, Soyoun; Lee, Dong ki

doi:10.5012/bkcs.2009.30.8.1827

Cited by 55 publications

(3 citation statements)

References 18 publications

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“…This makes it possible to detect and analyze the tumor cells without known biomarkers. To date, numerous aptamers for diverse cell lines have been generated, such as those against lymphocytic leukemia, − myeloid leukemia, glioblastoma, ,, colon cancer, − liver cancer, − breast cancer, − lung cancer, − cervical cancer, , and ovarian cancer. , Third, the target molecules specifically bound by aptamers can be identified to discover new biomarkers for disease diagnosis and therapy. The cell surface markers identified by cell-SELEX and aptamer-based targeted proteomics have been summarized in other reviews. , Additionally, many cell-SELEX variants have been developed, including cell-internalization SELEX for selecting aptamers with cellular internalization capability, , 3D cell-SELEX, tissue-SELEX, − and even in vivo -SELEX for selecting robust aptamers in mimicked or natural complex physiological environments. , …”

Section: Aptamer Evolution For Circulating Target Detectionmentioning

confidence: 99%

Aptamer-Based Detection of Circulating Targets for Precision Medicine

et al. 2021

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The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide realtime, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

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Section: Aptamer Evolution For Circulating Target Detectionmentioning

confidence: 99%

Aptamer-Based Detection of Circulating Targets for Precision Medicine

et al. 2021

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“…In breast cancer aptamers are gaining momentum, and they find usage in therapy, as well as in the detection of diagnostic and prognostic markers such as aberrant HER-2 forms [112,113], α-estrogen receptor status [114], vascular endothelial growth factor (VEGF) [115], osteopontin [116], Michigan Cancer Foundation-7 (MCF-7) cells [117], anterior gradient homolog 2 (AGR-2) protein [118].…”

Section: Medical Clinical Applicationsmentioning

confidence: 99%

Emerging Designs of Electronic Devices in Biomedicine

et al. 2020

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A long-standing goal of nanoelectronics is the development of integrated systems to be used in medicine as sensor, therapeutic, or theranostic devices. In this review, we examine the phenomena of transport and the interaction between electro-active charges and the material at the nanoscale. We then demonstrate how these mechanisms can be exploited to design and fabricate devices for applications in biomedicine and bioengineering. Specifically, we present and discuss electrochemical devices based on the interaction between ions and conductive polymers, such as organic electrochemical transistors (OFETs), electrolyte gated field-effect transistors (FETs), fin field-effect transistor (FinFETs), tunnelling field-effect transistors (TFETs), electrochemical lab-on-chips (LOCs). For these systems, we comment on their use in medicine.

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“…We chose ImProm-II, SuperScript IV (SSIV), TGIRT-III, Marathon RT (MaRT), and BST 3.0 DNA polymerase (BST) for these comparisons. ImProm-II originated from avian myeloblastosis virus (AMV) RT and has been used frequently in successful aptamer and ribozyme selections by our group ( Alam et al 2018 ; Gruenke et al 2020 , 2022 ) and others ( Kang et al 2009 ; Rahimi and Bitan 2010 ; Dua et al 2018 ). SSIV (and its predecessor SSIII) originated from Moloney murine leukemia virus (M-MLV) and is also commonly used in aptamer and ribozyme selections ( Moretti and Müller 2014 ; Saha et al 2018 ; Ning et al 2019 ; Pressman et al 2019 ; Strobel et al 2019 ; Akoopie et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Minimizing amplification bias during reverse transcription for in vitro selections

Lucas

Gruenke

Burke

2023

RNA

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Systematic Evolution of Ligands through EXponential enrichment (SELEX) is widely used to identify functional nucleic acids, such as aptamers and ribozymes. Ideally, selective pressure drives enrichment of sequences that display the function of interest (binding, catalysis, etc). However, amplification biases from reverse transcription can overwhelm this enrichment and leave some functional sequences at a disadvantage, with cumulative effects across multiple rounds of selection. Libraries that are designed to include structural scaffolds can improve selection outcomes by sampling sequence space more strategically, but they are also susceptible to such amplification biases, particularly during reverse transcription. Therefore, we tested five reverse transcriptases (RTs) – ImProm-II, Marathon RT (MaRT), TGIRT-III, SuperScript IV (SSIV), and BST 3.0 DNA polymerase (BST) – to determine which enzymes introduced the least bias. We directly compared cDNA yield and processivity for these enzymes on RNA templates with varying degrees of structure under various reaction conditions. In these analyses, BST exhibited excellent processivity, generated large quantities of full length cDNA product, displayed little bias among templates with varying structure and sequence, and performed well on long, highly structured viral RNAs. Additionally, six RNA libraries containing either strong, moderate, or no incorporated structural elements were pooled and competed head-to-head in six rounds of an amplification-only selection without external selective pressure using either SSIV, ImProm-II, or BST during reverse transcription. High-throughput sequencing established that BST maintained the most neutral enrichment values, indicating low inter-library bias over the course of six rounds, relative to SSIV and ImProm-II, and it introduced minimal mutational bias.

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Isolation of RNA Aptamers Targeting HER-2-overexpressing Breast Cancer Cells Using Cell-SELEX

Cited by 55 publications

References 18 publications

Aptamer-Based Detection of Circulating Targets for Precision Medicine

Aptamer-Based Detection of Circulating Targets for Precision Medicine

Emerging Designs of Electronic Devices in Biomedicine

Minimizing amplification bias during reverse transcription for in vitro selections

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