The measurement of protein-protein interactions (PPI) drives both our understanding of cancer development and routinely contributes to its clinical management. Both discovery and diagnostics increasingly rely on multiplexed assays for PPI. Protein microarrays provide a powerful approach to identify PPI efficiently in high- throughput. They allow proteome-scale screening with low sample consumption and are compatible with testing clinical material. With support from IMAT, we developed an innovative method for producing protein microarrays called nucleic acid programmable protein arrays (NAPPA) that produces properly folded proteins in a human milieu with consistent yields, just-in-time for the assay. NAPPA has proven to be an accurate and flexible tool for studying both novel PPI and patient immune responses. However, like all protein microarrays, NAPPA is subject to binding kinetics of surface-bound proteins, non-specific background binding and the limited dynamic range of fluorescence. Here, we propose the development of a next-generation, liquid-phase protein microarray platform, Multiplex In Solution Protein Array (MISPA), which exploits the extraordinary dynamic range of nucleic acid measurement and its wide availability in both research and clinical labs. We have developed a unique method to produce and barcode individual proteins, which can then interact in solution with a test molecule or clinical sample to separate targets from background. The barcodes are amplified and then assessed quantitatively by next generation sequencing (NGS) or qPCR. Because separate experiments can themselves be barcoded, multiple experiments can be combined and all the results determined in a single NGS run. We will test the feasibility of MISPA by investigating protein-protein interactions in the B-cell receptor (BCR) pathway, which is a prime target for cancer therapy and responsible for many B-cell malignancies. It provides an excellent test system because it includes both well-studied interactions and many unknown interactions awaiting exploration. We will probe 100 members of the BCR pathway with 10 key query proteins and analyze their interactions by NGS. We also propose to implement a robust, multiplexed qPCR-based diagnostic tool for studying immune responses in pathogen-induced cancers. We will focus on oropharyngeal carcinomas (OPC), which have been linked to human papillomavirus (HPV) infection. The proteomes of 10 different serotypes of HPV will be barcoded and tested against HPV positive OPC serum samples and control samples (N=20 each). This method expands on the key innovations of our NAPPA platform that included, programmability to test virtually any protein, in human milieu to encourage function, just-in-time protein production and equimolar protein display, and will also include new innovations including solution-phase binding kinetics, expanded dynamic range, compatibility with clinical diagnostics, reduced non-specific background, and multiplexed experimentation.
Measuring protein interactions is important in cancer biology and diagnostics. We propose to develop a novel tool in which we produce DNA barcoded proteins and incubate with many molecules to find new targets, using DNA sequencing. This will create a fast, sensitive, robust tool that is compatible with clinical diagnostics.