Abstract 2857: Digital nanoneedle biosensor technology for proteome-wide biomarker discovery
Authors: Quan Qimin , Ritchey Joshua , Clenow Mark , Wilkinson Joe , Geanacopoulos John , Boyce John 
Published: September 2020

Abstract
Understanding diseases and related biological processes at the proteome level will lead to the discovery of biomarkers for early diagnostics, enable drug development, patient selection, and treatment monitoring. Thus, there is an increasing demand for a more comprehensive and quantitative interrogation of the proteome at higher sensitivity, wider dynamic range, lower cost, and higher throughput than is currently possible by mass spectrometry or traditional immunoassays.
NanoMosaic is a digital immunoassay technology that achieves fg/ml level sensitivity, whole-proteome level multiplexing capability and 7 logs of dynamic range. It overcomes the sensitivity and dynamic range limitations posed by traditional protein arrays and mass spectrometry. The NanoMosaic technology is powered by silicon nanoneedle biosensors that are densely integrated on a plate and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a label-free biosensor, functionalized with capture antibodies, and changes its scattering spectrum when an antigen binds to its surface. Each analyte specific sensing area consists a total of ~24k nanoneedles divided into a digital region (~20k nanoneedles), an analog region (~3k nanoneedles) and a fabrication control region (~1k nanoneedles). The colors of all nanoneedles are imaged in a single shot with a low-cost color camera. The digital nanoneedles provide the single molecule sensitivity. Therefore, at ultra-low concentration when antigens captured by the nanoneedles follow Poisson statistics, the number of antigens can be quantitated by counting the presence or absence of color changes of individual nanoneedles in a binary fashion. As the protein concentrations increase, the counts increase accordingly and achieve saturation when all nanoneedles capture more than one protein. Above the saturation concentration, an adjacent section of analog nanoneedles perform quantitative analysis based on the level of color change, thus providing a wider dynamic range beyond the digital counting concentration ranges. We have demonstrated various assays on the NanoMosaic platform, in particular, a tau assay at 50fg/mL sensitivity, which serves as a potential biomarker for Alzheimer's disease. Each single analyte area, including both digital and analog sensors, is less than 500um. Therefore, ultrahigh level multiplex can be achieved by parallelizing the detection in a microarray format, while maintaining the same level of sensitivity and dynamic range. An ultrahigh-multiplex proteome wide assay only requires a ~70mm area with a total of 5 billion nanoneedles.
In conclusion, proteome-wide quantification and discovery of biomarkers can be performed in a single experiment, with high levels of multiplex and sensitivity on the NanoMosaic platform. Our technology enables the next frontier in biomarker discovery and proteome-wide interrogation which will lead to early diagnostics and more comprehensive understanding of diseases.
Citation Format: Qimin Quan, Joshua Ritchey, Mark Clenow, Joe Wilkinson, John Geanacopoulos, John Boyce. Digital nanoneedle biosensor technology for proteome-wide biomarker discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2857.