Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma

Eva Bräunlein, Gaia Lupoli, Franziska Füchsl, Esam T. Abualrous, Niklas De Andrade Krätzig, Dario Gosmann, Lukas Wietbrock, Sebastian Lange, Thomas Engleitner, Huan Lan, Stefan Audehm, Manuel Effenberger, Melanie Boxberg, Katja Steiger, Yinshui Chang, Kai Yu, Cigdem Atay, Florian Bassermann, Wilko Weichert, Dirk H. BuschRoland Rad, Christian Freund, Iris Antes, Angela M. Krackhardt

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Background Neoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized medicine, although many aspects of their quality and associated immune responses are not yet well understood. In a case study of metastatic malignant melanoma, we aimed to perform an in-depth characterization of neoantigens and respective T-cell responses in the context of immune checkpoint modulation. Methods Three neoantigens, which we identified either by immunopeptidomics or in silico prediction, were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient's immune repertoire recognizing these antigens. TCRs were compared in vitro by multiparametric analyses including functional avidity, multicytokine secretion, and cross-reactivity screenings. A xenograft mouse model served to study in vivo functionality of selected TCRs. We investigated the patient's TCR repertoire in blood and different tumor-related tissues over 3 years using TCR beta deep sequencing. Results Selected mutated peptide ligands with proven immunogenicity showed similar binding affinities to the human leukocyte antigen complex and comparable disparity to their wild-type counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs recognizing these antigens demonstrated distinct patterns in functionality and frequency. TCRs with lower functional avidity showed at least equal antitumor immune responses in vivo. Moreover, they occurred at high frequencies and particularly demonstrated long-term persistence within tumor tissues, lymph nodes and various blood samples associated with a reduced activation pattern on primary in vitro stimulation. Conclusions We performed a so far unique fine characterization of neoantigen-specific T-cell responses revealing defined reactivity patterns of neoantigen-specific TCRs. Our data highlight qualitative differences of these TCRs associated with function and longevity of respective T cells. Such features need to be considered for further optimization of neoantigen targeting including adoptive T-cell therapies using TCR-transgenic T cells.

Original languageEnglish
Article numbere002754
JournalJournal for ImmunoTherapy of Cancer
Issue number9
StatePublished - 12 Sep 2021
Externally publishedYes


  • CD8-positive T-lymphocytes
  • adaptive immunity
  • adoptive
  • antigens
  • immunologic
  • immunotherapy
  • neoplasm
  • receptors


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