Identification of shared TCR sequences from T cells in human breast cancer Using emulsion RT-PCR

Daniel J. Munson, Colt A. Egelston, Kami E. Chiotti, Zuly E. Parra, Tullia C. Bruno, Brandon L. Moore, Taizo A. Nakano, Diana L. Simons, Grecia Jimenez, John H. Yim, Dmitri V. Rozanov, Michael T. Falta, Andrew P. Fontenot, Paul R. Reynolds, Sonia M. Leach, Virginia F. Borges, John W. Kappler, Paul T. Spellman, Peter P. Lee, Jill E. Slansky

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


Infiltration of T cells in breast tumors correlates with improved survival of patients with breast cancer, despite relatively few mutations in these tumors. To determine if T-cell specificity can be harnessed to augment immunotherapies of breast cancer, we sought to identify the alpha-beta paired T-cell receptors (TCRs) of tumor-infiltrating lymphocytes shared between multiple patients. Because TCRs function as heterodimeric proteins, we used an emulsion-based RT-PCR assay to link and amplify TCR pairs. Using this assay on engineered T-cell hybridomas, we observed ∼85% accurate pairing fidelity, although TCR recovery frequency varied. When we applied this technique to patient samples, we found that for any given TCR pair, the dominant alpha- or beta-binding partner comprised ∼90% of the total binding partners. Analysis of TCR sequences from primary tumors showed about fourfold more overlap in tumor-involved relative to tumor-free sentinel lymph nodes. Additionally, comparison of sequences from both tumors of a patient with bilateral breast cancer showed 10% overlap. Finally, we identified a panel of unique TCRs shared between patients' tumors and peripheral blood that were not found in the peripheral blood of controls. These TCRs encoded a range of V, J, and complementarity determining region 3 (CDR3) sequences on the alpha-chain, and displayed restricted V-beta use. The nucleotides encoding these shared TCR CDR3s varied, suggesting immune selection of this response. Harnessing these T cells may provide practical strategies to improve the shared antigen-specific response to breast cancer.

Original languageEnglish (US)
Pages (from-to)8272-8277
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number29
StatePublished - Jul 19 2016


  • Breast cancer
  • Emulsion rt-PCR
  • High-throughput sequencing
  • T-cell receptors
  • T-cell repertoire profiling

ASJC Scopus subject areas

  • General


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