 APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistenceJingyi Xie,
Daniel G. Chen,
William Chour,
Rachel H. Ng,
Rongyu Zhang,
Dan Yuan,
Jongchan Choi,
Michaela McKasson,
Pamela Troisch,
Brett Smith,
Lesley Jones,
Andrew Webster,
Yusuf Rasheed,
Sarah Li,
Rick Edmark,
Sunga Hong,
Kim M. Murray,
Jennifer K. Logue,
Nicholas M. Franko,
Christopher G. Lausted,
Brian Piening,
Heather Algren,
Julie Wallick,
Andrew T. Magis,
Kino Watanabe,
Phil Mease,
Philip D. Greenberg,
Helen Chu,
Jason D. Goldman,
Yapeng Su and
James R. Heath ()
Nature Communications, 2025, vol. 16, issue 1, 1-15 Abstract: Abstract Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. We leverage this comprehensive dataset to integrate with peptide antigen properties, TCR CDR3 sequences, and T cell phenotypes to show that distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and T cell persistence. This analysis suggests that CD8 T cell phenotype following antigen stimulation is at least partially deterministic, rather than the result of stochastic biological properties. Date: 2025 Downloads: (external link) Related works: Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56659-3 Ordering information: This journal article can be ordered from DOI: 10.1038/s41467-025-56659-3 Access Statistics for this article Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie More articles in Nature Communications from Nature |
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