Expediting the Biomarker Discovery Process Through a Novel Bead-Based Aptamer Capture Platform

PROJECT SUMMARY: Fannin Innovation Studio is developing a new discovery proteomics platform called the Unified Process that identifies potential biomarkers in biological samples and simultaneously selects their affinity reagents (Raptamers). Currently, the translation of biomarkers from discovery to clinical utilization has been low; to address this problem, the Unified Process seeks to commercialize a rapid, high-throughput platform that establishes a powerful linkage between mass-spectrometry-based and affinity-based approaches to allow for early assay development for use in the validation of the identified potential biomarkers. A key component of the Unified Process utilizes Raptamer combinatorial library beads, which are next- generation oligonucleotides with several chemical modifications attached to the DNA bases and/or in the backbone. The major steps to the Unified Process include: 1) Raptamer library beads are incubated with samples specific to a disease phenotype and control samples, followed by sorting by flow cytometry, with each sorted bead having unique Raptamer sequences that will be bound to the yet unidentified protein; 2) Raptamer oligonucleotides are released from the sorted beads and pulled down with biotinylated biofluid in a multiplexed step; 3) Raptamer oligonucleotides are identified by sequencing and are synthesized and used to pull down biomarker candidates from the biological samples; and 4) LC/MS/MS identifies the biomarker candidates. Notably, the resulting Raptamers are immediately available for downstream applications to precisely quantify the identified potential biomarkers in formats such as enzyme-linked oligonucleotide assays (ELONAs) and selected reaction monitoring (SRM) MS. The availability of Raptamer affinity reagents to potential biomarkers so early in the discovery phase will accelerate the verification and subsequent validation of candidates, saving significant time and expense translating discoveries into the clinic. This proposed project is focused integrating, optimizing, and fully characterizing this novel approach for successful implementation of the Unified Process. The Phase I aim are: Aim 1: Optimize the Unified Process to decrease the lead time in identification of proteins. The goal is to decrease the lead time of this process by at least 25% with a goal of 50% by successfully moving directly from bead sorting to mass spectrometry. Aim 2: Demonstrate retrieval of known biomarkers from various sample types using the optimized Unified Process. The goals are to determine the limit of detection of the potential protein biomarkers in various tissue types and to identify potential Raptamers that can be new affinity reagents for these existing biomarkers. Successful completion of this study will demonstrate proof of concept for the Unified Process and will position us for an SBIR Phase II project to characterize unknown biomarkers in various disease types. Ultimately, Fannin Innovation Studio plans to commercialize the Unified Process by selling it as a service and retaining the rights to commercialize the resulting Raptamers for use in potential research and clinical diagnostic assays.