In The November Issue:Blackwater Falls West Virginia

  • Base Pair Welcomes a New Scientist – Marsha Kowal
  • Biosensor Survey Ending Soon
  • Aptamer Inhibition of Allergic Reaction


Base Pair Welcomes Marsha Kowal

The Base Pair team is pleased to welcome Marsha Kowal. Marsha is a biomedical engineer with extensive research experience combining cell biology with engineering innovation. She earned her Ph.D. from Cornell University where she investigated the relationship between aging and cardiovascular disease development. Prior to Cornell, Marsha earned her B.S. in bioengineering from Oregon State University where she was also a NCAA track athlete.

“I’m excited to apply my multidisciplinary background to the development of novel aptamer technologies at Base Pair.” -Marsha Kowal

Biosensor Survey

Base Pair is currently developing several aptamer-based biosensors using the R100 platform from Nanomedical Diagnostics. Vote Now and tell us which biosensor features and performance criteria are most important to you.

Aptamer Inhibition of Allergic Reaction

Researchers at the University of Bonn in Germany have demonstrated the use of selective RNA aptamers to block allergic response in a mouse model by inhibiting the chemokine signaling that causes lymphocyte migration. This is a promising new strategy for the development of therapeutics for a wide range of chronic diseases involving inflammation.

Chemokine-Mediated Allergic Response

Cytokines and chemokines are small proteins that play a key role in the intracellular signaling and immune cell recruitment that cause inflammation. More than 44 chemokines and 23 chemokine receptors are involved in immune regulation. While chemokine production and signaling is important for inflammation in cases of infection, abnormal chemokine production or signaling can cause unnecessary and problematic inflammation. Identifying targets linked to immune-related diseases and tactics for modifying their activity is critical for the development of new treatments. (2) In mouse models, the chemokine CCL17 has been associated with contact hypersensitivity, atopic dermatitis, inflammatory bowel disease, atherosclerosis, and arthritis. In humans, elevated CCL17 levels have been linked to atopic dermatitis, allergic rhinitis, asthma, and bronchopulmonary aspergillosis. Researchers at the University of Bonn in Germany recently selected RNA aptamers that inhibit CCL17-mediated allergic response. (1, 2)

Selection and Modification of Anti-Murine CCL17 (TARC) Aptamers

Aptamers are short, single-strands of DNA (~30 to 100 nucleotides) that form unique tertiary structures which can selectively bind a specific target. A starting library of trillions of DNA or RNA sequences goes through many rounds of a process called SELEX to identify target-selective aptamers. Researchers at the University of Bonn in Germany recently selected RNA aptamers that inhibit CCL17-mediated allergic response. The researchers initiated the SELEX process with a 2’deoxy-2’-fluoro pyrimidine-modified RNA library for enhanced protection against nuclease degradation. Ten rounds of SELEX were performed. Next-generation sequencing and filter retention analysis were used to identify two CCL17-selective aptamers, MF11 and MF35. The aptamers were later truncated prior to synthesis for in vivo applications, yielding aptamers of fewer than 50 nucleotides, MF11.46 and MF35.47. Selectivity of truncated aptamers was confirmed using surface plasmon resonance (SPR). (1)

Inhibition of Allergic Response In Vitro and In Vivo

While selective binding is important, functional activity is the ultimate goal in custom aptamer selection. A transwell migration assay was used to test the ability of the aptamers to neutralize CCL17 activity in vitro. The assay was based on the chemotactic migration of BW5147.3 thymoma cells toward CCL17. In the transwell migration assay, both aptamers MF11 and MF35 inhibited transmigration at doses of 7.5 pmol/well. MF11 showed 10-fold higher efficiency, with inhibition at only 0.75 pmol/well. (1)

To assess aptamer performance in vivo, the researchers examined the effect of aptamers on contact hypersensitivity. Mice were challenged with 2,4-dinitro-1-fluorobenxene (DNFB), causing infiltration of CD45+ leukocytes, CD8+ T cells, and ear-swelling. Injection of either aptamer significantly reduced observed ear-swelling and infiltration of CD45+ leukocytes, as determined by flow cytometry. Interestingly, the MF35.47 aptamer was more efficient than the MF11.46 aptamer at inhibiting CD8+ T cell infiltration and reducing the ear-swelling response in vivo. (1) This differential performance in vitro and in vivo highlights the importance of evaluating aptamers for specific applications in functional assays.

Clinical Application of Aptamers in Allergy

Aptamers offer several advantages over traditional monoclonal antibodies as potential therapeutic agents. Unlike antibodies, which typically rely on an immune response, aptamers can be selected against toxic and non-immunogenic compounds. Aptamers can be selective for a single point mutation or compounds that differ by a single functional group. Their small size may enable binding to domains that are not accessible to large antibodies. (3) Enhanced accessibility to dermal and epidermal compartments make aptamers ideal candidates for skin-related disorders. Aptamers also tend to be far less immunogenic than antibodies, reducing potential side effects. While some researchers have questioned in vivo stability of aptamers due to nucleases, the modified RNA aptamers in this study were stable in human serum for up to ten days. (1) Improvements in aptamer selection and modification and demonstration of the clinical utility of aptamers in animal models have paved the way for human studies involving therapeutic aptamers.

Custom Aptamer Selection

Base Pair has selected aptamers to a wide range of targets, including cytokines, serum proteins, metabolites, small molecule drugs, and viral proteins. Tell us a bit about your project so that we can propose an aptamer selection strategy for you.

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1. Fulle, et al. RNA aptamer recognizing murine CCL17 inhibit TCell chemotaxis and reduce contact hypersensitivity in vivo. Molecular Therapy. 2017.

2. Turner, M.D., et al. Cytokines and chemokines: At the crossroads of cell signalling and inflammatory disease. Biochimica et Biophysica Acta. 2014. 1843(11):2563-2582.

3.  Zhou, J. and John Rossi. Aptamers as targeted therapeutics: current potential and challenges. Nature Reviews: Drug Discovery. 2017. 16(3):181-202.