Günter Mayer

Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT): a highly multiplexed aptamer-based biomarker discovery platform

Günter Mayer^1,2, Valeriy Domenyuk¹, Zhenyu Zhong¹, Adam Stark¹, Jie Wang¹, Sonal Tonapi, Heather O’Neill¹, Nianqing Xiao¹, Mark R. Miglarese¹, Michael Famulok^1,2,3, and David B. Spetzler¹

¹Caris Life Sciences, Phoenix, AZ;

²LIMES Program Unit Chemical Biology & Medicinal Chemistry, University of Bonn, Germany;

³Chemical Biology Max-Planck-Fellowship Group, Center of Advanced European Studies and Research, Bonn, Germany.

Here we report on Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT) as a ssDNA aptamer-based highly multiplexed biomarker discovery platform and we report its potential utility in breast cancer diagnostics. We enriched a ssDNA library of 10¹² oligonucleotides (ODNs) for interacting with blood plasma exosomes. Enrichment was confirmed by comparing binding profiles of the starting and the enriched ODN libraries to plasma exosomes using Next Generation Sequencing (NGS), qPCR, flow cytometry and mass spectrometry. To further refine the enriched libraries, we generated a sub-library containing 2000 individual ODNs and profiled 500 plasma samples from 206 breast cancer biopsy positive (BC+), 177 biopsy negative (BC-) and 117 self-declared healthy donors (H). A Random Generalized Linear Model was used to build a case/control classifier and yielded Area Under a ROC Curve (AUC)-values of 0.58 (BC+ vs. all controls), 0.63 (BC+ vs. BC-) and 0.6 (BC+ vs. H) in a 5-fold cross-validation analysis. The most informative 50 ODNs significantly improved performance compared to the original 2000: AUC=0.62 (BC+ vs. all), 0.66 (BC+ vs. BC-) and 0.67 (BC+ vs. H). In summary, the ADAPT-platform identifies and measures thousands of ODNs that form signatures by their association with differentially expressed biomolecules in their native states. These data indicate that ADAPT may have promising utility as a diagnostic tool.