Aptamer Fields

With the expiration of key aptamer selection patents, aptamer use is quickly expanding into many fields.  Aptamers are increasingly being pursued as alternatives to antibodies in many areas of diagnostics and therapeutics. The ability to generate aptamers against small, non-immunogenic metabolites and toxic pathogens creates unique opportunities in drug testing and food safety. The generation of selective aptamers to toxic compounds creates uses for aptamers in environmental testing and bioterrorism. The ability to bind or block sites on specific proteins or compounds in vivo without triggering a biological response creates new opportunities for in vivo diagnostics and therapeutics and the potential use of aptamers as stabilizers in a wide range of consumer products. A brief overview of a few of the many growing aptamer fields is provided below.

 

Diagnostics

Diagnostic assays for infectious diseases typically involve direct detection of pathogens, viruses, or pathogen-related toxins. Many pathogen-related detection methods do not meet current needs. They lack sensitivity, are too time-consuming, are too costly, or require analysis equipment that prevents field-based testing.  The ability to generate high-affinity aptamers selective for toxic compounds is being utilized to produce a new generation of aptamer-based diagnostic assays for bacterial pathogens (S. aureas, Salmonella typhimurium, C. albicans, E. coli), bacterial toxins (toxin A from Clostridium difficile), and viruses (hepatitis C, avian influenza, West Nile virus, dengue fever, and HIV-1).  A wide range of formats are being employed for aptamer-based tests, including biosensors, ELASA (ELISA-like) assays, and lateral flow assays (LFAs). Aptamer stability makes them ideal for point-of-care testing in many locations.

Diagnostic assays in oncology, autoimmune disease, and other clinical areas frequently involve biomarkers, cell-associated or secreted proteins that are up-regulated or down-regulated in disease. While some biomarker-based diagnostic assays measure a single analyte, multiplex testing platforms are increasingly being used to simultaneously test for a panel of biomarkers and analyze profiles. Biomarker profiles are used to detect disease, monitor disease progression and treatment, and identify appropriate treatment options. Researchers are increasingly turning to aptamers for use in biomarker-based diagnostic assays. Aptamers have shown a high degree of selectivity for both circulating and tissue-based cancer markers. Aptamer-based assays and arrays eliminate many of the non-specific binding and cross-reactivity issues associated with traditional antibody-based platforms. Learn More

Chandola, C. et al. Application of aptamers in diagnostics, drug-delivery and imaging. Sept. 2016. 41(3):535-561. doi:10.1007/s12038-016-9632-y

Drugs of Abuse

Overdoses in the U.S. from illicit opioids increased 73% in 2015, while the incidence of opioid withdrawal in newborns increased 5-fold in the U.S. from 2000 to 2012. [1,2] In response to the growing use and abuse of a wider range of opioids, Base Pair has successfully developed a number of aptamers that selectively bind to opioids and opioid metabolites. Noroxycodone and norhydrocodone are unique metabolites of oxycodone and hydrocodone. Because these metabolites are not administered directly to drug users, their presence in the urine has a direct correlation to use of hydrocodone or oxycodone. [3,4,5] Metabolite detection in the urine of neonates indicates maternal use of hydrocodone or oxycodone during pregnancy. Base Pair performed an aptamer selection project for the National Institutes of Health using a urine-like synthetic buffer formulation to generate aptamers with high selectivity and affinity to noroxycodone and norhydrocodone, which also bind in natural urine. Learn More

  1. Almasy, Steve. “Opioid epidemic is getting worse says CDC.” CNN. ​9 Dec 2016, http://www.cnn.com/2016/12/08/health/opiod-deaths-2015/index.html. Accessed 12 Dec 2016.
  2. Drash, Wayne. “Report finds skyrocketing rate of babies going through opiate withdrawal.” CNN. 13 Dec 2016, http://www.cnn.com/2016/12/12/health/heroin-opiates-babies-new-research/index.html. Accessed 13 Dec 2016.
  3. Cone, E.J., et al. Urine testing for norcodeine, norhydrocodone, and noroxycodone facilitates interpretation and reduces false negatives. Forensic Science International. 2010;198:58-61​
  4. Fang, W.B., et al. Determination of oxycodone, noroxycodone, and oxymorphone by high-performance liquid chromatography-electrosprsay ionization-tandem mass spectrometry in human matrices: in vivo and in vitro applications. Journal of Analytical Toxicology. 2013;37(6):337-44.​
  5. Valtier, S., et al. Excretion profile of hydrocodone, hydromorphone, and norhydrocodone in urine following single dose administration of hydrocodone to healthy volunteers. Journal of Analytical Toxicology. 2012. doi:10.1093/jat/bks058.

 

Environmental Testing

Aptamers offer a novel option for the creation of screening tools for toxins and chemicals in soil and water. Aptamer stability is ideal for field-based testing in a wide range of conditions. The ability to design aptamers to target toxic compounds and small, non-immunogenic molecules enables the production of screening assays for a wide range of environmentally-hazardous compounds. Aptamer-based sensors for detection of lead and mercury in soil and pond samples are in development. [3] New aptamer-based assays are being created for the military to detect bioterror agents, including neurotoxins, viruses, and bacteria.

Aptamer-based tests to monitor pesticides and run-off chemicals can be applied in agriculture and agrochemicals. Aptamers can be used to monitor pesticide levels, detect the presence of particularly harmful organophosphorus pesticides, and possible remove harmful pesticide residues from the environment. [2] Overuse of antibiotics encourages the formation of antibiotic-resistant bacteria. Aptamers to small molecule antibiotics can be developed to measure antibiotics in food-producing livestock. Aptamers can be used to measure the presence of antibiotics in farm waste and human sewage and could potentially be used to filter antibiotics in waste-processing to reduce the release of antibiotics into the environment. [1]  Learn More

  1. Nadia Nikolaus and Beate Strehlitz, DNA-Aptamers Binding Aminoglycoside Antibiotics, Sensors, 2014, 14: 3737-3755. doi: 10/3390/s140203737.
  2. Wang, L. et al. Selection of DNA aptamers that bind to four organophosphorus pesticides. Biotechnology Letters. Msay 2012. 34(5):869-874. doi:10.1007/s10529-012-0850-6
  3. Xu, D. et al. Application of aptamers in food safety. Chinese Journal of Analytical Chemistry. June 2011. 39(6):925-933. doi.org/10.1016/S1872-2040(10)

 

Food Safety

The ability to generate highly selective aptamers to toxic and non-immunogenic compounds make them ideal candidates for reagent and assay development in the area of food safety. Unlike antibodies, aptamers can be developed with specificity for small molecules and other non-immunogenic compounds. Aptamers have been used to measure specific antibiotics and detect residual organic dyes in foods. Aptamers can also be developed to bind specific pathogens.  Aptamers have been used successfully to detect SEB (Staphylococcal Enterotoxin B) in wheat samples and to screen for Listeria, E. coli, and other pathogenic food contaminants.

Xu, D. et al. Application of aptamers in food safety. Chinese Journal of Analytical Chemistry. June 2011. 39(6):925-933. doi.org/10.1016/S1872-2040(10)60447-1.

 

Therapeutics

Nucleic acid aptamers with high affinity and selectivity can be raised against a wide range of targets, including targets that are toxic or non-immunogenic. Additionally, their small size, stability, controlled chemical synthesis, and low immunogenicity make aptamers attractive therapeutic agents. Aptamer-based therapeutics are taking many forms. In some cases, aptamer-ligand binding can have therapeutic effects. Some aptamers are being optimized for allosteric regulation, where ligand binding induces a conformational change in the aptamer that creates an active or inactive state. Aptamers with enzymatic activity are being developed for the in vivo regulation of gene expression and have been demonstrated in E. coli, yeast, and mammalian cells. [1,2] Aptamers that successfully target and enter NSCLC cells and induce apoptosis are in development as potential therapeutics. [3]

Aptamers are also being developed as drug carriers for specific cell targeting. An aptamer selective for prostate-specific membrane antigen (PSMA) has recently been complexed with the anti-cancer drug doxorubicin to provide targeted drug delivery, increasing the ability of the drug to reach cancer cells and decreasing off-target effects. [1] The aptamer synthesis process offers reduced cost, reduced regulatory concerns, and improved batch-to-batch consistency when compared to traditional antibody-based therapeutics. Aptamers may also be a more cost-effective and more consistent alternative for purification of biopharmaceuticals. Learn More

  1. Jo, Hunho, et al. Aptamer-nanoparticle complexes as powerful diagnostic and therapeutic tools. Experimental & Molecular Medicine. 48,e230. 6 May 2016. doi:10.1038/emm.2016.44
  2. Vinkemborg, J.L. , et al. Aptamers for allosteric regulation. Nature Chemical Biology. 7,519-27. 2011. doi: 10.1038/nchembio.609
  3. Xu, Li, et al. Cellular internalization and cytotoxicity of aptamers selected from lung cancer cell. American Journal of Biomedical Sciences. 2013. 5(1):47-58. doi:10.5099/aj130100047.