Aptamers as Diagnostic Tools in Cancer

Ciancio, Dario Ruiz; Vargas, Mauricio R; Thiel, William H.; Bruno, Martín A.; Giangrande, Paloma H.; Mestre, María Belén

doi:10.3390/ph11030086

Cited by 75 publications

(61 citation statements)

References 142 publications

(155 reference statements)

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“…Aptamers that selectively bind to specific targets have extensively been demonstrated to be promising as a diagnostic tool for disease detection through molecular recognition, and have been prominently investigated. 21,45,[49][50][51][52][53][54][55] In this study, an aptamer specific to the RBD region of the SARS-CoV-2 spike protein was selected as the probe for the detection of the SARS-CoV-2 in saliva.…”

Section: Resultsmentioning

confidence: 99%

Detection of the SARS-CoV-2 spike protein in saliva with Shrinky-Dink© electrodes

Zakashansky¹,

Imamura

Salgado

et al. 2020

Preprint

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Section: Resultsmentioning

confidence: 99%

Detection of the SARS-CoV-2 spike protein in saliva with Shrinky-Dink© electrodes

Zakashansky¹,

Imamura

Salgado

et al. 2020

Preprint

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“…However, low concentrations of cancer biomarkers in serum or plasma, mixed with other proteins make the early cancer diagnosis quite tricky. Additionally, these methods could be labor-intensive and time-consuming [ 25 ]. Therefore, due to their higher sensitivity i.e., the ability to detect quite low quantities of their targets [ 7 , 8 ], aptamers have become an emerging and promising tool for cancer diagnosis and imaging.…”

Section: Aptamers In Cancer Diagnosismentioning

confidence: 99%

“…This can be done by replacing the 2′-OH with several functional groups like amino (NH 2 ), O -methyl (OCH 3 ), or fluoro (F) groups. Another approach is to utilize inverted dT residue for capping the 3′ end of oligonucleotides [ 25 , 26 ], to improve the stability of aptamers. The recently developed SELEX methods shortened the time from weeks to hours and from multiple rounds to even a single round.…”

Section: Introductionmentioning

confidence: 99%

Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

2020

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Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.

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“…Aptamers are RNA or short single-stranded DNA molecules, which fold into a three-dimensional structure and bind different types of target molecules such as proteins [3], small molecules [4], toxins [5], ions [6], and cell surfaces [7]. Owing to the wide variety of possible target molecules, aptamers are commonly used for therapeutics [8], clinical diagnostics [9], the high-throughput multi-protein measurement [10], imaging [11], and biosensors [12].…”

Section: Introductionmentioning

confidence: 99%

FSBC: fast string-based clustering for HT-SELEX data

Kato

Ono

Minagawa³

et al. 2020

BMC Bioinformatics

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Background: The combination of systematic evolution of ligands by exponential enrichment (SELEX) and deep sequencing is termed high-throughput (HT)-SELEX, which enables searching aptamer candidates from a massive amount of oligonucleotide sequences. A clustering method is an important procedure to identify sequence groups including aptamer candidates for evaluation with experimental analysis. In general, aptamer includes a specific target binding region, which is necessary for binding to the target molecules. The length of the target binding region varies depending on the target molecules and/or binding styles. Currently available clustering methods for HT-SELEX only estimate clusters based on the similarity of full-length sequences or limited length of motifs as target binding regions. Hence, a clustering method considering the target binding region with different lengths is required. Moreover, to handle such huge data and to save sequencing cost, a clustering method with fast calculation from a single round of HT-SELEX data, not multiple rounds, is also preferred. Results: We developed fast string-based clustering (FSBC) for HT-SELEX data. FSBC was designed to estimate clusters by searching various lengths of over-represented strings as target binding regions. FSBC was also designed for fast calculation with search space reduction from a single round, typically the final round, of HT-SELEX data considering imbalanced nucleobases of the aptamer selection process. The calculation time and clustering accuracy of FSBC were compared with those of four conventional clustering methods, FASTAptamer, AptaCluster, APTANI, and AptaTRACE, using HT-SELEX data (>15 million oligonucleotide sequences). FSBC, AptaCluster, and AptaTRACE could complete the clustering for all sequence data, and FSBC and AptaTRACE performed higher clustering accuracy. FSBC showed the highest clustering accuracy and had the second fastest calculation speed among all methods compared. Conclusion: FSBC is applicable to a large HT-SELEX dataset, which can facilitate the accurate identification of groups including aptamer candidates. Availability of data and materials: FSBC is available at http://www.aoki.ecei.tohoku.ac.jp/fsbc/.

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Aptamers as Diagnostic Tools in Cancer

Cited by 75 publications

References 142 publications

Detection of the SARS-CoV-2 spike protein in saliva with Shrinky-Dink© electrodes

Detection of the SARS-CoV-2 spike protein in saliva with Shrinky-Dink© electrodes

Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

FSBC: fast string-based clustering for HT-SELEX data

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