Defining T cell receptor repertoires using nanovial-based affinity and functional screening

Doyeon Koo; Zhiyuan Mao; Robert Dimatteo; Natalie Tsubamoto; Miyako Noguchi; Jami McLaughlin; Wendy Tran; Sohyung Lee; Donghui Cheng; Joseph de Rutte; Giselle Burton Sojo; Owen N Witte; Dino Di Carlo

doi:10.1101/2023.01.17.524440

Defining T cell receptor repertoires using nanovial-based affinity and functional screening

bioRxiv [Preprint]. 2023 Jan 20:2023.01.17.524440. doi: 10.1101/2023.01.17.524440.

Authors

Doyeon Koo¹, Zhiyuan Mao², Robert Dimatteo³, Natalie Tsubamoto¹, Miyako Noguchi⁴, Jami McLaughlin⁴, Wendy Tran⁴, Sohyung Lee³, Donghui Cheng⁵, Joseph de Rutte^{1

6}, Giselle Burton Sojo⁴, Owen N Witte^{2

4

5

7

8

9}, Dino Di Carlo^{1

6

10

11}

Affiliations

¹ Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA.
² Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA.
³ Department of Chemical and Biomolecular Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA.
⁴ Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA.
⁵ Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles; Los Angeles, CA 90095, USA.
⁶ Partillion Bioscience; Los Angeles, CA 90095, USA.
⁷ Molecular Biology Institute, University of California, Los Angeles; Los Angeles, CA 90095, USA.
⁸ Jonsson Comprehensive Cancer Center, University of California, Los Angeles; Los Angeles, CA 90095, USA.
⁹ Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA.
¹⁰ Department of Mechanical and Aerospace Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA.
¹¹ California NanoSystems Institute; Los Angeles, CA 90095, USA.

Abstract

The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.

Publication types

Preprint

Abstract

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