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Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

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Abstract

Substantial regressions of metastatic lesions have been observed in up to 70% of patients with melanoma who received adoptively transferred autologous tumor-infiltrating lymphocytes (TILs) in phase 2 clinical trials1,2. In addition, 40% of patients treated in a recent trial experienced complete regressions of all measurable lesions for at least 5 years following TIL treatment3. To evaluate the potential association between the ability of TILs to mediate durable regressions and their ability to recognize potent antigens that presumably include mutated gene products, we developed a new screening approach involving mining whole-exome sequence data to identify mutated proteins expressed in patient tumors. We then synthesized and evaluated candidate mutated T cell epitopes that were identified using a major histocompatibility complex–binding algorithm4 for recognition by TILs. Using this approach, we identified mutated antigens expressed on autologous tumor cells that were recognized by three bulk TIL lines from three individuals with melanoma that were associated with objective tumor regressions following adoptive transfer. This simplified approach for identifying mutated antigens recognized by T cells avoids the need to generate and laboriously screen cDNA libraries from tumors and may represent a generally applicable method for identifying mutated antigens expressed in a variety of tumor types.

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Figure 1: Response of TIL 2098 to candidate epitopes identified from autologous tumors.
Figure 2: Response of TIL 2369 to candidate epitopes identified from autologous tumors.
Figure 3: Response of TIL 3309 to candidate epitopes identified from autologous tumors.
Figure 4: IFN-γ ELISPOT responses of TIL and PBMCs obtained before and after autologous TIL transfer.

Change history

  • 14 May 2013

     In the version of this article initially published online, the second sentence of the abstract stated, “In addition, 40% of patients treated in a recent trial experienced complete regressions of all measurable lesions lasting between 5 and 9 years after treatment3.” The correct statement should read, “In addition, 40% of patients treated in a recent trial experienced complete regressions of all measurable lesions for at least 5 years following TIL treatment3.” The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank B. Van den Eynde (Ludwig Institute) for providing HEK293 cells transfected with immunoproteasomal subunits and S. Schwarz and R. Fisch for assisting with experiments.

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Contributions

P.F.R. designed and developed the experimental screening system, analyzed data and drafted the manuscript. Y.-C.L. and M.E.-G. performed experiments evaluating TIL responses against candidate mutated peptides and analyzed results. Y.F.L. cloned and sequenced gene products encoding candidate epitopes identified by exomic sequencing and analyzed results. J.K.T., C.G., E.T., J.C.L. and P.C. carried out bioinformatic analyses. J.G. provided advice on exomic sequencing, prepared samples for sequencing and carried out validation studies using Sanger sequencing. Y.S. provided advice on sequencing of DNA isolated from tumor and normal cells and assisted with data analysis. S.A.R. helped design the studies and edited the manuscript.

Corresponding author

Correspondence to Paul F Robbins.

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The authors declare no competing financial interests.

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Robbins, P., Lu, YC., El-Gamil, M. et al. Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells. Nat Med 19, 747–752 (2013). https://doi.org/10.1038/nm.3161

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