Identification of Amino Acids and Nucleotides Required for Interaction Between BAFF‐R and its RNA Aptamer

Abstract

Current cancer therapies such as surgery, radiation, and chemotherapy can leave residual tumor cells and have off‐target effects. Aptamers are used in a type of targeted cancer therapy that more precisely identify and attack cancer cells, while leaving unaffected cells unharmed. In B‐cell malignancies, such as non‐Hodgkins lymphoma, there is increased expression of B‐cell activating factor (BAFF) and its receptor (BAFF‐R). Upon binding to its receptor, BAFF increases B‐cell proliferation and survival, allowing cancer cells to proliferate faster than normal B‐cells. An RNA aptamer has been identified that binds BAFF‐R with high specificity and affinity, blocking BAFF binding. The aptamer has also been shown to successfully deliver therapeutic siRNA that is taken up by the cell and causes significant knock down of its mRNA. The objective of this study is to identify the essential nucleotides and amino acids required for interaction between BAFF‐R and its RNA aptamer by synthesizing and purifying the RNA aptamer using PCR and in vitro transcription, and synthesizing and purifying WT BAFF‐R and mutants. Gel‐shift assays and RNase protection assays will be used to identify amino acids of BAFF‐R and the nucleotides of its RNA aptamer that are key for their interaction. This contribution is significant because it will provide the details that allow for fine‐tune engineering of aptamers to be used in target cancer therapies, thus improving quality of life and more successful clinical outcomes for patients will B‐cell malignancies. The proposed research is innovative, in our opinion, because this is a new way to target B‐cells that is currently underdeveloped and therefore under utilized.