Abstract 19: Proteome-wide biomarker discovery using digital MosaicNeedles
Authors: Qimin Quan, Joshua Ritchey, Joe Wilkinson, John Geanacopoulos, Alaina Kaiser, John Boyce
Journal: Cancer Research (2021)

Abstract Changes in transcript levels detected by transcriptome profiling have been widely used as a surrogate for proteomics. However, recent studies have shown accumulating evidence that phenotypes of diseases that show correlations with protein levels cannot be explained by transcript levels. Hence a proteome-wide biomarker search will provide valuable information for cancer research that is not achievable from a strictly genomic approach. NanoMosaic is a digital immunoassay technology that uses a sub-100 nm nanoneedle sensor to detect single molecules. Over a billion nanoneedles are fabricated on a silicon substrate, thus named MosaicNeedlesTM, and formatted into 96, 384 or 1536 isolated well configurations at standard microplate dimensions. Each nanoneedle is a label-free biosensor, that is functionalized with capture antibodies. Each individual nanoneedle shifts its scattering spectrum when an antigen binds to it. The spectrum shift is further enhanced using a chemical amplification process. At low concentrations, the binding events of molecules to the MosaicNeedlesTM follow a Poisson distribution which insure that the number of molecules can be quantitated by counting the number of nanoneedles that display a spectrum change. Imaging automation is achieved by TessieTM instrument that reads the entire MosaicNeedlesTM and analyzes the color spectrum of individual nanoneedles. High multiplexing level up to 50 analytes can be achieved by parallelizing the detection in a microarray format within each well. NanoMosaic uses a hypothesis-free approach to construct its protein biomarker discovery panel, also known as proteome-wide association study (PWAS) panel. Individual protein analytes included in the PWAS panel are evenly spaced across the exome. Therefore, a sub-group of the entire human proteome or secretome can be interrogated in a hypothesis-free way before the entire proteome or a reflexive protein sub-group is interrogated. This approach addresses the limitations of the availability of the affinity reagents (antibodies, nanobodies, aptamers and etc.) that would be needed to simultaneously interrogate the whole proteome. Once valuable targets of interest are identified by running the PWAS-panel against a cohort of samples, mechanism studies can then be done using pathway specific panels whose design can be informed by previous PWAS results. In conclusion, NanoMosaic provides a solution to conduct a proteome-wide search for disease relevant biomarkers using its hypothesis-free PWAS-panels. The use of MosaicNeedlesTM provides higher sensitivity, wider dynamic range, lower cost and higher throughput than is currently possible by mass spectrometry or traditional immunoassay methods. Citation Format: Qimin Quan, Joshua Ritchey, Joe Wilkinson, John Geanacopoulos, Alaina Kaiser, John Boyce. Proteome-wide biomarker discovery using digital MosaicNeedles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 19.