SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen
- 1School of Basic Medical Sciences, Tsinghua Medicine, Tsinghua University
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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BibTeX
@misc{li2026seeker,
title = {{SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen}},
author = {S. Li and L. Lin and W. Wu and B. Liu and H. Ji and Z. Guo and Y. Liu and J. Wu and B. Liu and L. Zhong and X. Wang and H. Xu and H. Qi},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.25.753432},
url = {https://www.biorxiv.org/content/10.64898/2026.09.25.753432v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen
AU - S. Li
AU - L. Lin
AU - W. Wu
AU - B. Liu
AU - H. Ji
AU - Z. Guo
AU - Y. Liu
AU - J. Wu
AU - B. Liu
AU - L. Zhong
AU - X. Wang
AU - H. Xu
AU - H. Qi
PY - 2026
DA - 2026/09/25
PB - bioRxiv
DO - 10.64898/2026.09.25.753432
UR - https://www.biorxiv.org/content/10.64898/2026.09.25.753432v1
AB - 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.
ER -