Aptamer Publications
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Articles
A new method for the reproducible development of aptamers (Neomers). Meehan C, Hamilton EL, Mansour CG, Lecocq S, Drake CJ, Rodrigues E, Penner G (2024) PLoS One.
Abstract
The development of aptamers has been almost exclusively performed based on the SELEX method since their inception. While this method represents a powerful means of harnessing the in vitro evolution of sequences that bind to a given target, there are significant constraints in the design. The most significant constraint has been the reliance on counter selection on off-targets to drive specificity. Counter selection has not been as effective at driving aptamer specificity as the presence of immune tolerance, the capacity of the immune system to remove antibodies that bind to host targets, is for antibody development. This deficiency has constrained the commercial efficacy of aptamers to date. These limitations have been addressed with our design of a novel platform for aptamer identification. This new design is based on what we refer to as a Neomer library with sixteen random nucleotides interspersed with fixed sequences. The fixed sequences are designed to minimize the potential for hybridization, such that secondary structure is driven by the random nucleotides. The use of sixteen random nucleotides reduces the possible library sequences to 4.29 × 109. This enables the application of the same sequences to either the same target or different targets while maintaining a high level of structural diversity. In effect, this introduces the capacity for reproducibility in aptamer selection and an in-silico approach to replicating immune tolerance. We provide here an overview of the new method and a description of the performance of aptamers selected for interleukin 6 developed using this approach.
A reproducible approach for the use of aptamer libraries for the identification of Aptamarkers for brain amyloid deposition based on plasma analysis. Meehan C, Lecocq S, Penner G (2024) PLoS One.
Abstract
An approach for the agnostic identification and validation of aptamers for the prediction of a medical state from plasma analysis is presented in application to a key risk factor for Alzheimer’s disease. brain amyloid deposition. This method involved the use of a newly designed aptamer library with sixteen random nucleotides interspersed with fixed sequences called a Neomer library. The Neomer library approach enables the direct application of the same starting library on multiple plasma samples, without the requirement for pre-enrichment associated with the traditional approach. Eight aptamers were identified as a result of the selection process and screened across 390 plasma samples by qPCR assay. Results were analysed using multiple machine learning algorithms from the Scikit-learn package along with clinical variables including cognitive status, age and sex to create predictive models. An Extra Trees Classifier model provided the highest predictive power. The Neomer approach resulted in a sensitivity of 0.88. specificity of 0.76. and AUC of 0.79. The only clinical variables that were included in the model were age and sex. We conclude that the Neomer approach represents a clear improvement for the agnostic identification of aptamers (Aptamarkers) that bind to unknown biomarkers of a medical state.
Development of novel aptamers for low-density lipoprotein particle quantification. Klapak D, Broadfoot S, Penner G, Singh A, Inapuri E (2018) PLoS ONE.
Abstract
Cardiovascular disease (CVD) remains the leading cause of death worldwide. Low-density lipoprotein cholesterol (LDL-C) is commonly used for CVD risk assessment; however, recent research has shown LDL particle (LDL-P) number to be a more sensitive indicator of CVD risk than both LDL-C and non-high-density lipoprotein cholesterol (HDL-C). Described herein are five single stranded DNA aptamers with dissociation constants in the low picomolar range specific to LDL-P and its subfractions. Furthermore, a set of antisense sequences have been developed and characterized that are capable of binding to the best aptamers and undergoing displacement by LDL-P for use in a simple, affordable diagnostic assay.
Aptamers as biomarkers for neurological disorders. Proof of concept in trangenic mice. Lecocq S, Spinella K, Dubois B, Lista S, Hampel H, Penner G (2018) PloS One.
Abstract
The act of selecting aptamers against blood serum leads to deep libraries of oligonucleotide sequences that bind to a range of epitopes in blood. In this study we developed an enriched aptamer library by performing positive selection against a pool of blood serum samples from transgenic mice (P301S) carrying the human tau gene and counter selecting against pooled blood serum from negative segregant (wild type) mice. We demonstrated that a large proportion of the aptamer sequences observed with next generation sequence (NGS) analysis were the same from selection round 5 and selection round 6. As a second step, we applied aliquots of the selection round 5 enriched library to blood serum from 16 individual mice for a single round of selection. Each of these individual libraries were characterized through NGS analysis and the changes in relative frequency in aptamers from transgenic mice versus wild type were used to construct a diagnostic fingerprint of the effect of the action of the transgene on the composition of blood serum. This study serves as a model for similar applications with human subjects.
Improved Aptamers for the Diagnosis and Potential Treatment of HER2-Positive Cancer Marlies Gijs, Gregory Penner , Garth B. Blackler , Nathalie R.E.N. Impens, Sarah Baatout , André Luxen and An M. Aerts, Pharmaceuticals 2016, 9, 29;
Abstract
Aptamers provide a potential source of alternative targeting molecules for existing antibody diagnostics and therapeutics. In this work, we selected novel DNA aptamers targeting the HER2 receptor by an adherent whole-cell SELEX approach. Individual aptamers were identified by next generation sequencing and bioinformatics analysis. Two aptamers, HeA2_1 and HeA2_3, were shown to bind the HER2 protein with affinities in the nanomolar range. In addition, both aptamers were able to bind with high specificity to HER2-overexpressing cells and HER2-positive tumor tissue samples. Furthermore, we demonstrated that aptamer HeA2_3 is being internalized into cancer cells and has an inhibitory effect on cancer cell growth and viability. In the end, we selected novel DNA aptamers with great potential for the diagnosis and possible treatment of HER2-positive cancer
Selection, activity, and nuclease stabilization of cross-neutralizing DNA aptamers targeting HSV-1 and HSV-2. Schump MD, Bernstein DI, Bravo FJ, Neff CP., Virology. 2024; 589.
Abstract
Cross-neutralizing aptamers targeting both HSV-1 and HSV-2 were developed by selecting against the ectodo mains of glycoprotein D (gD) from both viruses in parallel as well as sequentially using the SELEX method. Since gD facilitates viral invasion, sterically blocking the host-receptor interaction prevents infection. Candidate aptamers were screened, and lead aptamers were identified that exhibited exceptional neutralizing activity against both viruses in vitro. The specificity of the aptamers was confirmed by comparing their activity to scrambled versions of themselves. Modifications of the lead compounds were tested to define critical motifs to guide development. Stability of the aptamers was increased using phosphorothioate backbone linkages, and 2’methoxy substitutions of terminal and key internal bases. Aptamers were applied in a guinea pig vaginal HSV-2 infection model and found to reduce both the viral load of infected animals and the severity of the resulting disease. These results suggest that cross-neutralizing aptamers can be developed into on-demand antiviral inerventions effective against both HSV-1 and HSV-2.
Determination of ochratoxin a with a DNA aptamer. Cruz-Aguado JA, Penner G.,J Agric Food Chem. 2008 Nov 26;56(22):10456-61
Abstract
This work describes the identification of an aptamer that binds with high affinity and specificity to ochratoxin A (OTA), a mycotoxin that occurs in wheat and other foodstuffs, and a quantitative detection method for OTA based on the use of this aptamer. Aptamers are single-stranded oligonucleotides selected in vitro to bind to molecular targets. The aptamer selected in this work exhibited a dissociation constant in the nanomolar range and did not bind compounds with structures similar to OTA such as N-acetylphenylalanine or warfarin. The aptamer bound with a 100-fold less affinity to ochratoxin B. The selected aptamers could be used for the determination of ppb quantities of OTA in naturally contaminated wheat samples. Further work is ongoing to broaden the application demonstrated here with the development of sensors, affinity columns, and other analytical systems for field and laboratory determination of this toxin in food and agricultural products.
Fluorescence polarization based displacement assay for the determination of small molecules with aptamers. Cruz-Aguado JA, Penner G.Anal Chem. 2008 Nov 15;80(22):8853-5
Abstract
The conversion of an aptamer-target binding event into a detectable signal is an important step in the development of aptamer-based sensors. In this work, we show that the displacement of a fluorescently labeled oligo from the aptamer by the target can be detected by fluorescence polarization (FP). We used Ochratoxin A (OTA), a small organic molecule (MW = 403) as a case study. A detection limit of 5 nM OTA was achieved. The method presented here provides an advantage over fluorophore-quenching systems and other steady-state fluorescence approaches in that no modification of the aptamer or the target is required. Additionally, the signal is produced by the displacement event itself, so no further aggregation or conformational events have to be considered. This analytical method is particularly useful for small targets, as for large targets a direct measurement of the FP change of a labeled aptamer upon binding can be used to determine the concentration of the target. The results presented here demonstrate that aptamers and inexpensive labeled oligos can be used for rapid, sensitive, and specific determination of small molecules by means of FP.
Detection of Breast Cancer Cells Using Acoustics Aptasensor Specific to HER2 Receptors, Biosensors2019, 9(2), 72
Abstract
Detection of the breast cancer cells is important for early diagnosis of the cancer. We applied thickness shear mode acoustics method (TSM) for detection of SK-BR-3 breast cancer cells using DNA aptamers specific to HER2 positive membrane receptors. The biotinylated aptamers were immobilized at the neutravidin layer chemisorbed at gold surface of TSM transducer. Addition of the cells resulted in decrease of resonant frequency, fs, and in increase of motional resistance, Rm. Using gold nanoparticles (AuNPs), modified by aptamers it was possible improving the limit of detection (LOD) that reached 550 cells/mL, while without amplification the sensitivity of the detection of SK-BR-3 cells was 1574 cells/mL. HER2 negative cell line MDA-MB-231 did not resulted in significant changes of fs. The viability studies demonstrated that cells are stable at experimental conditions used during at least 8 h. AuNPs were not toxic on the cells up to concentration of 1 μg/mL.
INSIGHT-preAD study group, & Alzheimer Precision Medicine Initiative (APMI) Penner, G., Lecocq, S., Chopin, A., Vedoya, X., Lista, S., Vergallo, A., Cavedo, E., Lejeune, F. X., Dubois, B., Hampel, H., (2021).
Aptamarker prediction of brain amyloid-β status in cognitively normal individuals at risk for Alzheimer’s disease. PloS one, 16(1), e0243902
Blood-based diagnostics of Alzheimer’s disease. Expert review of molecular diagnostics, 19(7), 613–621. Penner, G., Lecocq, S., Chopin, A., Vedoya, X., Lista, S., Vergallo, A., Lejeune, F. X., & Hampel, H. (2019).
Aptamers as biomarkers for neurological disorders. Proof of concept in transgenic mice. PloS one, 13(1), e0190212. Lecocq, S., Spinella, K., Dubois, B., Lista, S., Hampel, H., & Penner, G. (2018).
Development of novel aptamers for low-density lipoprotein particle quantification. PloS one, 13(10), e0205460. Klapak, D., Broadfoot, S., Penner, G., Singh, A., & Inapuri, E. (2018).
Improved Aptamers for the Diagnosis and Potential Treatment of HER2-Positive Cancer. Pharmaceuticals (Basel, Switzerland), 9(2), 29. Gijs, M., Penner, G., Blackler, G. B., Impens, N. R., Baatout, S., Luxen, A., & Aerts, A. M. (2016).
Determination of ochratoxin a with a DNA aptamer. Journal of agricultural and food chemistry, 56(22), 10456–10461. Cruz-Aguado, J. A., & Penner, G. (2008).
Patents
Penner, G. (2023). A method for reproducible aptamer selection used to identify aptamers that bind to unknown biomarkers. (WO/2023/137558).
Penner, G. (2023). A method for reproducible aptamer selection using closed sequence solution spaces. (WO/2023/137559).
Mousses, S., Azorsa, D., Feldheim, D. Heil, J., Tran, N., Penner, G. (2023). Compositions for inhibiting growth of targeted cells. (WO/2022/235971).
Mousses, S., Azorsa, D., Feldheim, D. Heil, J., Tran, N., Penner, G. (2023). Multitargeting RNA immunotherapy compositions. (WO/2022/235957).
Mousses, S., Azorsa, D., Feldheim, D. Heil, J., Tran, N., Penner, G. (2023). SiRNA constructs for inhibiting gene expression in targeted cancer cells. (WO/2022/235975).
Velasquez, J.E., Rupard, S.C., Trejo, A.V., Pitz, A.M., Schmeichel, K.L, Swigart, E.N., Penner, G., et. al. (2023). Aptamers for health care applications. (WO/2023/114800).
Velasquez, J.E., Rupard, S.C., Trejo, A.V., Pitz, A.M., Schmeichel, K.L, Swigart, E.N., Penner, G., et. al. (2023). Aptamers for health care applications. (WO/2023/114801).
Velasquez, J.E., Rupard, S.C., Trejo, A.V., Pitz, A.M., Schmeichel, K.L, Swigart, E.N., Penner, G., et. al. (2023). Aptamers for health care applications. (WO/2023/114802).
Shannon, R.J., Penner, G. (2022). Aptamers against clostridium difficile, compositions comprising aptamers against clostridium difficile and methods of using the same. (WO/2022/120004).
Inapuri, E., Singh, A. Penner, G. (2022). Aptamers for measuring lipoprotein levels. (WO/2019/010341).
Shannon, R.J., Penner, G. (2021). Aptamers against sars-cov-2, compositions comprising aptamers against sars-cov-2 and methods using the same. (WO/2021/202440).
Penner, G. (2021). Method for the selection of aptamers for unbound targets. (WO/2017/035666).
Penner, G. (2020). Early detection of precursor of alzhiemer’s disease. (WO/2020/079248).
Velasquez, J.E., Trejo, A.V., Marsh, J.M., Penner, G. (2020). Aptamers for hair care applications. (WO/2020/005325).
Velasquez, J.E., Trejo, A.V., Penner, G., Jones, S.D. (2020). Aptamers for odor control applications. (WO/2020/214784).
Velasquez, J.E., Trejo, A.V., Sagel, P.A., Penner, G. (2019). Aptamers for oral care applications. (WO/2019/032795A1).
Penner, G. (2012). A method for the selection of DNA ligands for a molecular target. (WO/2012/113072).
Cruz-Aguado, J.A., Penner, G. (2011). A method and apparatus for lateral flow determination of analyte concentration. (WO/2011/032278).
Cruz-Aguado, J.A., Penner, G. (2011). Method for determining the presence and concentration of analytes using a nucleic acid ligand and rare earth element. (WO/2011/014945).
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