Fannin Innovation Studio is developing a new discovery proteomics platform called theUnified Process that identifies potential biomarkers in biological samples and simultaneously selects their affinityreagents (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 thatestablishes a powerful linkage between mass-spectrometry-based and affinity-based approaches to allow forearly 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 thebackbone. The major steps to the Unified Process include: 1) Raptamer library beads are incubated with samplesspecific to a disease phenotype and control samples, followed by sorting by flow cytometry, with each sortedbead having unique Raptamer sequences that will be bound to the yet unidentified protein; 2) Raptameroligonucleotides are released from the sorted beads and pulled down with biotinylated biofluid in a multiplexedstep; 3) Raptamer oligonucleotides are identified by sequencing and are synthesized and used to pull downbiomarker 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 theidentified potential biomarkers in formats such as enzyme-linked oligonucleotide assays (ELONAs) and selectedreaction monitoring (SRM) MS. The availability of Raptamer affinity reagents to potential biomarkers so early inthe discovery phase will accelerate the verification and subsequent validation of candidates, saving significanttime and expense translating discoveries into the clinic.This proposed project is focused integrating, optimizing, and fully characterizing this novel approach forsuccessful implementation of the Unified Process. The Phase I aim are: Aim 1: Optimize the Unified Processto decrease the lead time in identification of proteins. The goal is to decrease the lead time of this processby at least 25% with a goal of 50% by successfully moving directly from bead sorting to mass spectrometry. Aim2: Demonstrate retrieval of known biomarkers from various sample types using the optimized UnifiedProcess. The goals are to determine the limit of detection of the potential protein biomarkers in various tissuetypes 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 positionus for an SBIR Phase II project to characterize unknown biomarkers in various disease types. Ultimately, FanninInnovation Studio plans to commercialize the Unified Process by selling it as a service and retaining the rightsto commercialize the resulting Raptamers for use in potential research and clinical diagnostic assays.
Public Health Relevance Statement: PROJECT NARRATIVE
Biomarkers have the potential to reduce healthcare costs by aiding in early disease diagnosis and by predicting
disease outcome and response to treatment; however, to date, only a small number of biomarkers are used
routinely in the clinic. This proposal seeks to commercialize a new biomarker discovery platform that will enable
rapid, high-throughput screening and detection of potential biomarker candidates. Additionally, a significant
benefit compared to other biomarker discovery platforms is that this process allows for simultaneous detection
of the reagents that can be used to develop diagnostic assays for clinical validation, which will facilitate clinical
adoption of biomarker strategies.
Project Terms:
