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

Deciphering which antigens activate T cell receptors (TCRs) is a crucial challenge in immunology, and researchers have now introduced SEEKER, a groundbreaking platform to address this issue. This innovative system comprises three key components: a Jurkat-derived T-APC cell (referred to as TAPCell) that simultaneously expresses a TCR and a peptide-MHC (pMHC) combination from separate libraries, alongside an NFAT activation reporter.

To ensure isolated clonal expansion, the TAPCells are encapsulated within a thermos-reversible hydrogel. This allows for the accurate reading of recognition as intraclonal activation. Additionally, dual-asymmetric PCR plays a pivotal role by linking TCR- and pMHC-encoding sequences into a heritable unit. This enables progressive enrichment of hits throughout the screening process, even without prior knowledge of the specific antigens being targeted.

The SEEKER platform is capable of interrogating an astounding ~10^8 TCR-pMHC combinations per run, making it an incredibly powerful tool in the field. In a recent case study, the platform was applied to screen joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries. This screening process successfully validated 53 TCR-peptide pairs, revealing extensive cross-recognition of both self and common viral epitopes.

More importantly, the study uncovered highly polyreactive T cells that recognize up to 80 autoantigens, shedding light on the role of virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.