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Published September 21, 2019 | Submitted + Supplemental Material
Journal Article Open

MATE-Seq: Microfluidic Antigen-TCR Engagement Sequencing


Adaptive immunity is based on peptide antigen recognition. Our ability to harness the immune system for therapeutic gain relies on the discovery of the T cell receptor (TCR) genes that selectively target antigens from infections, mutated proteins, and foreign agents. Here we present a method that selectively labels peptide antigen-specific CD8+ T cells using magnetic nanoparticles functionalized with peptide–MHC tetramers, isolates these specific cells within an integrated microfluidic device, and directly amplifies the TCR genes for sequencing. Critically, the identity of the peptide recognized by the TCR is preserved, providing the link between peptide and gene. The platform requires inputs on the order of just 100 000 CD8+ T cells, can be multiplexed for simultaneous analysis of multiple peptides, and performs sorting and isolation on chip. We demonstrate 1000-fold sensitivity enhancement of detecting antigen-specific TCRs relative to bulk analysis and simultaneous capture of two virus antigen-specific TCRs from a population of T cells.

Additional Information

© 2019 The Royal Society of Chemistry. The article was received on 06 Jun 2019, accepted on 05 Aug 2019 and first published on 08 Aug 2019. Sequencing data is available at the Sequence Read Archive under project PRJNA546025. AHCN is supported by a Banting Postdoctoral Fellowship from the Government of Canada. AMX is supported by a Ruth L. Kirschstein F32 Postdoctoral Fellowship from the National Cancer Institute (1F32CA213966-01). This work was supported by the Parker Institute for Cancer Immunotherapy, by a Caltech-GIST project grant, by the Washington State CARE Foundation, and by the National Cancer Institute (grant 5U54CA199090-05, PI Heath). We thank Drs. Jesse Zaretsky and Antoni Ribas for providing donor specimens. Author contributions: AHCN, SP, AMX, WJN, KG, MTB, JC, SY, DB, and JRH designed the experiments. AHCN, SP, WJN, KG, WC did the experiments. AHCN, SP, AMX, WJN and JRH analyzed the data. AHCN, AMX, and JRH wrote the paper. Conflicts of interest: JRH and DB are founders of PACT Pharma, which is a company seeking to develop personalized T cell therapies for immuno-oncology, and which has licensed technology related to that described here.

Attached Files

Submitted - 706606.full.pdf

Supplemental Material - c9lc00538b1_si.pdf

Supplemental Material - c9lc00538b2.zip

Supplemental Material - c9lc00538b3.mp4

Supplemental Material - c9lc00538b4.mp4

Supplemental Material - c9lc00538b5.mp4


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August 19, 2023
October 20, 2023