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bioRxiv · 10.64898/2026.09.25.753432

SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen

Li, S.·Lin, L.·Wu, W.·Liu, B.·Ji, H.·Guo, Z.·Liu, Y.·Wu, J.·Zhong, L.·Wang, X.·Xu, H.·Qi, H.
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Abstract

Decoding which antigens activate a given T cell receptor (TCR) is a central challenge in immunology. We present SEEKER, a functional genome-scale library-on-library screening platform built on three elements: a Jurkat-derived T-APC cell (TAPCell) that combinatorially expresses one TCR and one peptide-MHC drawn from separate libraries together with an NFAT activation reporter; encapsulation of single TAPCells in a thermos-reversible hydrogel for isolated clonal expansion, so recognition is read out as intraclonal activation; and dual-asymmetric PCR that links TCR- and pMHC-encoding sequences into a heritable unit, enabling progressive hit enrichment over screening rounds. SEEKER interrogates ~10^8 TCR-pMHC combinations per run without prior knowledge. Screening joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries validated 53 TCR-peptide pairs, uncovered extensive cross-recognition of self and common viral epitopes, and revealed highly polyreactive T cells recognizing up to 80 autoantigens, implicating virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.

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Li, S., Lin, L., Wu, W., Liu, B., Ji, H., Guo, Z., Liu, Y., Wu, J., Zhong, L., Wang, X., Xu, H., Qi, H.. 2026-10-01. SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen. https://doi.org/10.64898/2026.09.25.753432

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