AGBT 2024: Mining the plasma proteome; a novel ultrasensitive and high-plex liquid biopsy platform reveals changes in biologically important low-abundance biomarkers

Abstract

The blood proteome holds substantial potential for advancing precision medicine, but it poses significant analytical challenges due to the lack of technologies capable of detecting the vast majority of plasma proteins present in very low concentrations. Here, we present NUcleic acid Linked Immuno-Sandwich Assay (NULISA™), which employs a dual capture and release mechanism to effectively reduce assay background noise and enhance the sensitivity of the proximity ligation assay by approximately 10,000 times, reaching attomolar level of detection. NULISA employs DNA-linked antibodies to convert immunocomplexes to reporter DNA molecules which can be quantified with quantitative real-time PCR (qPCR) or next-generation sequencing (NGS), enabling both ultra-high sensitivity and high multiplexing capacity. NULISA assays are fully automated on the ARGO™ HT System, a high-throughput precision proteomics platform that automates the entire workflow from sample to qPCR data or to a pooled NGS library.

Two high-plex NULISA panels: a 250-plex inflammation panel and a 120-plex central nervous system (CNS) disease panel were developed and tested on disease cohorts. The inflammation panel has the most comprehensive coverage of cytokines and chemokines and other immune-related proteins in a single panel and demonstrated superior sensitivity in detecting low-abundance proteins with high precision, enabling the detection of difficult-to-detect but biologically important low-abundance biomarkers in the blood of patients with autoimmune diseases and COVID-19. The CNS panel is the largest multiplex panel designed specifically for neurodegenerative diseases encompassing all key hallmarks of Alzheimer’s and has demonstrated the potential to identify both established and novel proteins associated with various neurodegenerative diseases that were previously challenging to detect in the blood.

In conclusion, NULISA uniquely combines ultra-high sensitivity and high multiplexing in a single platform, enabling focused in-depth analysis of the blood proteome. Automation on the ARGO HT system provides a high throughput and high precision proteomics platform, which should open doors to the low abundance portion of the proteome and provide new biological insights that may lead to a new generation of biomarkers for early disease detection and monitoring and eventually to novel therapeutic approaches.