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Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

Gee, Marvin H. and Han, Arnold and Lofgren, Shane M. and Beausang, John F. and Mendoza, Juan L. and Birnbaum, Michael E. and Bethune, Michael T. and Fischer, Suzanne and Yang, Xinbo and Gomez-Eerland, Raquel and Bingham, David B. and Sibener, Leah V. and Fernandes, Ricardo A. and Velasco, Andrew and Baltimore, David and Schumacher, Ton N. and Khatri, Purvesh and Quake, Stephen R. and Davis, Mark M. and Garcia, K. Christopher (2018) Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Cell, 172 (3). pp. 549-563. ISSN 0092-8674. PMCID PMC5786495. doi:10.1016/j.cell.2017.11.043.

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The immune system can mount T cell responses against tumors; however, the antigen specificities of tumor-infiltrating lymphocytes (TILs) are not well understood. We used yeast-display libraries of peptide-human leukocyte antigen (pHLA) to screen for antigens of “orphan” T cell receptors (TCRs) expressed on TILs from human colorectal adenocarcinoma. Four TIL-derived TCRs exhibited strong selection for peptides presented in a highly diverse pHLA-A∗02:01 library. Three of the TIL TCRs were specific for non-mutated self-antigens, two of which were present in separate patient tumors, and shared specificity for a non-mutated self-antigen derived from U2AF2. These results show that the exposed recognition surface of MHC-bound peptides accessible to the TCR contains sufficient structural information to enable the reconstruction of sequences of peptide targets for pathogenic TCRs of unknown specificity. This finding underscores the surprising specificity of TCRs for their cognate antigens and enables the facile identification of tumor antigens through unbiased screening.

Item Type:Article
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URLURL TypeDescription CentralArticle
Fischer, Suzanne0000-0003-4110-6576
Baltimore, David0000-0001-8723-8190
Quake, Stephen R.0000-0002-1613-0809
Garcia, K. Christopher0000-0001-9273-0278
Additional Information:© 2017 Elsevier Inc. Received 7 July 2017, Revised 30 October 2017, Accepted 22 November 2017, Available online 21 December 2017, Published: December 21, 2017. We thank Trevor Hinshaw and Chris Bolen for technical assistance; Jonathan Sockolosky, Naresha Saligrama, Fan Zhao, and Francesco Vallania for helpful discussions; Luke Lee for providing cell lines; and Molly Uyeda and Eric Smith for graphical designs. M.H.G. was supported by a Stanford Graduate Research Fellowship and an NIH grant (CA216926-01). M.T.B. was supported by a Jane Coffin Childs Postdoctoral Fellowship. J.L.M. was supported by an NIH award (CA175127). This work was supported by NIH grants (DK100739 to A.H.; AI103867 to K.C.G.; 32681-05 to D.B.), the Bill and Melinda Gates Foundation, the National Institute for Allergy and Infectious Diseases (1U19AI109662, U19AI057229, U54I117925, and 1R01AI125197 to P.K.), Dutch Cancer Society Queen Wilhelmina (2013-6122), and the K.G. Jebsen Foundation (to T.N.S.), the Howard Hughes Medical Institute (to K.C.G. and M.M.D.), and Parker Institute for Cancer Immunotherapy (to K.C.G. and M.M.D.). Author Contributions: M.H.G., A.H., K.C.G., and M.M.D. conceived of the project and wrote the manuscript. A.H. and M.H.G. conducted the single-cell T cell phenotyping, TCR sequencing, and yeast screening. M.H.G. also generated the yeast-display construct, conduced data analysis, and performed target validation. M.H.G., S.M.L., and J.L.M. developed the algorithms for predicting putative human targets from the deep-sequencing data. J.F.B. performed the patient exome sequencing. M.T.B. provided the F5 TCR used to optimize HLA-A∗02:01 display and validate ligand discovery. S.F. and M.E.B. helped design the yeast-display construct, and S.F. conducted yeast-display experiments. X.Y. conducted the yeast-display experiments and the surface plasmon resonance studies. R.G.-E. conducted T cell activation experiments for NKI2. D.B.B. performed immunohistochemistry on the patient tumor tissue. L.V.S. and R.A.F. provided conceptual insight and technical expertise. A.V. generated virus for TCR expression. M.E.B., D.B., S.R.Q., P.K., T.N.S., M.M.D., and K.C.G. supervised the research. All authors edited the manuscript. Declaration of Interests: M.H.G. and L.V.S. are co-founders of 3T Biosciences.
Funding AgencyGrant Number
Stanford UniversityUNSPECIFIED
Jane Coffin Childs Memorial Fund for Medical ResearchUNSPECIFIED
Bill and Melinda Gates FoundationUNSPECIFIED
Dutch Cancer Society Queen Wilhelmina2013-6122
K. G. Jebsen FoundationUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Parker Institute for Cancer ImmunotherapyUNSPECIFIED
Subject Keywords:T cell; T cell receptor; human leukocyte antigen; combinatorial biology; peptide library; peptides; antigens; ligand identification; single-cell sequencing; cancer
Issue or Number:3
PubMed Central ID:PMC5786495
Record Number:CaltechAUTHORS:20171221-152204867
Persistent URL:
Official Citation:Marvin H. Gee, Arnold Han, Shane M. Lofgren, John F. Beausang, Juan L. Mendoza, Michael E. Birnbaum, Michael T. Bethune, Suzanne Fischer, Xinbo Yang, Raquel Gomez-Eerland, David B. Bingham, Leah V. Sibener, Ricardo A. Fernandes, Andrew Velasco, David Baltimore, Ton N. Schumacher, Purvesh Khatri, Stephen R. Quake, Mark M. Davis, K. Christopher Garcia, Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes, Cell, Volume 172, Issue 3, 2018, Pages 549-563.e16, ISSN 0092-8674,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:84007
Deposited By: Tony Diaz
Deposited On:21 Dec 2017 23:53
Last Modified:18 Mar 2022 22:10

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