Solid-state nanopores and silicon nanomembranes for ultrasensitive protein biomarker detection

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Abstract Proteins in serum and urine provide diagnostic indications of early cancers, traumatic brain injury, and other life threatening conditions, but are difficult to detect at ultra-low concentrations. While ultrasensitive protein detection has been achieved using digital (i.e. molecular counting) ELISA (dELISA) platforms such as Quanterix’s SiMoA, these instruments require specialized and complex optics for single molecule detection, which is difficult to miniaturize. Solid-state nanopores (ssNPs) now offer an alternative digital sensing opportunity for protein biomarkers following our invention of Controlled Dielectric Breakdown (CBD) as an inexpensive method for single nanopore fabrication. Unlike the optical readout of dELISA platforms, ssNPs can provide a completely electronic solution for low-cost, point-of-care instruments that are needed to bring ultrasensitive diagnostics to low resource settings. Our proposal brings together an accomplished team with expertise in ssNP sensors, separations, microfluidics, and molecular diagnostics to solve the remaining technical challenges for ultrasensitive ssNP-based sensing. We will establish feasibility through a head-to-head comparison to the Quanterix SiMoA. The technical challenge of signal amplification will be solved by combining a new immunoassay that transduces every target protein biomarker in serum or urine to hundreds of 50nt 100 DNA proxies coupled to 60 nm gold nanoparticles (AuNP). This signal will then be concentrated in a microfluidic platform using ultrathin nanoporous silicon nitride (NPN) membranes that have a proven capacity to capture and concentrate AuNPs up to 10,000 fold. The proxies will be released from the NPN with UV light and will rapidly hybridize with DNA nanostructures that give robust signals in a ssNP sensor positioned only a few hundred micrometers away. The combined 106- fold increase in biomarker concentration will enable the ssNP to process signals from fM concentrations of protein biomarker in minutes. This novel instrument, which we’ve termed the catch and release for proxy enhancement ssNP (CRePE-ssNP), will be validated on two clinically relevant biomarker panels of requiring increasing enhancement factors: 1) urine biomarkers that predict bladder cancer immunotherapy efficacy; and 2) biomarkers in serum used to detect brain injury. Urine biomarkers will be drawn from the CyPRIT Nomogram panel which predict bladder cancer (BC) response to an inoculation with Bacillus Calmette-Guérin (BCG). Thresholds for this panel are in the low pM/high fM range. Our more challenging application will be the low fM level detection of TBI biomarkers (UCHL1, GFAP) in serum. Performance in both studies will be benchmarked against the SiMoA HD-1Analyzer from Quanterix.