nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome.

Existing high-plex protein measurement tools compromise on quantification, precision and cost efficiency. Here, to address this, we present nELISA, a platform that combines a DNA-mediated, bead-based sandwich immunoassay with advanced multicolor bead barcoding. Antibody pairs are preassembled on target-specific, barcoded beads, which ensures spatial separation between noncognate assays. Detection antibodies are tethered via flexible single-stranded DNA to enable efficient ternary sandwich formation. Detection is achieved through toehold-mediated strand displacement, where fluorescently labeled DNA oligos simultaneously untether and label detection antibodies. nELISA delivers sub-picogram-per-milliliter sensitivity across seven orders of magnitude. Using a 191-plex inflammation panel, we profiled cytokine responses in 7,392 peripheral blood mononuclear cell samples, generating ~1.4 million protein measurements and revealing over 440 robust cytokine responses, including previously unreported effects. nELISA thus provides a simple, scalable and cost-efficient solution for large-scale, high-fidelity phenotypic screening.