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Identification of a broad coverage HLA-DR degenerate epitope pool derived from carcinoembryonic antigen

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Abstract

CD4 T cells are important for anti-tumor immune responses. Aside from their role in the activation of CD8 T cells, CD4 T cells also mediate anti-tumor immune responses by recruiting innate immune effectors into the tumor microenvironment. Thus, the search for strategies to boost CD4 T cell immunity is an active area of research. Our goal in this study was to identify HLA-DR epitopes of carcinoembryonic antigen (CEA), a commonly over-expressed tumor antigen. HLA-DR epitopes of CEA were identified using the epitope prediction program, PIC (predicted IC50) and tested using in vitro HLA-DR binding assays. Following CEA epitope confirmation, IFN-γ ELIspot assays were used to detect existing immunity against the HLA-DR epitope panel of CEA in breast and ovarian cancer patients. In vitro generated peptide-specific CD4 T cells were used to determine whether the epitopes are naturally processed from CEA protein. Forty-three epitopes of CEA were predicted, 15 of which had high binding affinity for 8 or more common HLA-DR molecules. A degenerate pool of four, HLA-DR restricted 15 amino acid epitopes (CEA.24, CEA.176/354, CEA.488, and CEA.653) consisting of two novel epitopes (CEA.24 and CEA.488) was identified against which 40% of breast and ovarian cancer patients had pre-existent T cell immunity. All four epitopes are naturally processed by antigen-presenting cells. Hardy–Weinberg analysis showed that the pool is useful in ~94% of patients. Patients with breast or ovarian cancer demonstrate pre-existent immune responses to the tumor antigen CEA. The degenerate pool of CEA peptides may be useful for augmenting CD4 T cell immunity.

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Acknowledgments

The authors gratefully acknowledge the Mayo Clinic Comprehensive Cancer Center Immune Monitoring Core for performing the ELIspot assays, the Mayo Clinic Proteomics Research Center and Tissue and Cell Molecular Analysis Center (TACMA). The assistance of Corazon dela Rosa and Jennifer Childs is greatly appreciated. This work was supported by the Mayo Clinic Comprehensive Cancer Center, generous gifts from Martha and Bruce Atwater (KLK), K01-CA100764 (KLK), P50-CA116201 (JI), K12-CA090628 (KRK, LH), and R41-CA107590-01 (GI, KLK, JF).

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Author notes

  1. John D. Fikes

    Present address: Kalypsys, Inc., 10420 Waterridge Circle, San Diego, CA, 92121, USA

  2. Glenn Ishioka

    Present address: , 11516 Hadar Dr., San Diego, CA, 92126, USA

Authors and Affiliations

  1. Department of Immunology, College of Medicine, Mayo Clinic, 342C Guggenheim, 200 First St. SW, Rochester, MN, 55905, USA

    Lavakumar Karyampudi, Christopher J. Krco, Courtney L. Erskine, Chao Yu, Peter J. Wettstein & Keith L. Knutson

  2. Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA

    Kimberly R. Kalli, Lynn C. Hartmann, Karin Goodman & James N. Ingle

  3. Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA

    Matthew J. Maurer

  4. Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, 55905, USA

    Aziza Nassar

  5. Tumor Vaccine Group, Center for Translational Medicine in Women’s Health, Seattle, WA, 98195, USA

    Mary L. Disis

  6. Pharmexa-Epimmune, Inc., San Diego, CA, 92121, USA

    John D. Fikes, Melanie Beebe & Glenn Ishioka

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  1. Lavakumar Karyampudi
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Correspondence to Keith L. Knutson.

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L. Karyampudi and C. J. Krco are co-first authors. G. Ishioka and K. L. Knutson are co-senior authors.

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Karyampudi, L., Krco, C.J., Kalli, K.R. et al. Identification of a broad coverage HLA-DR degenerate epitope pool derived from carcinoembryonic antigen. Cancer Immunol Immunother 59, 161–171 (2010). https://doi.org/10.1007/s00262-009-0738-z

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  • DOI: https://doi.org/10.1007/s00262-009-0738-z

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