Supplementary Tables 1 - 4, Figures 1 - 2 from Peptide/MHC Tetramer–Based Sorting of CD8+ T Cells to a Leukemia Antigen Yields Clonotypes Drawn Nonspecifically from an Underlying Restricted Repertoire

Hunsucker, Sally A.; McGary, Colleen S.; Vincent, Benjamin G.; Enyenihi, Atim A.; Waugh, Jennifer P.; McKinnon, Karen P.; Bixby, Lisa M.; Ropp, Patricia A.; Coghill, James M.; Wood, William A.; Gabriel, Don A.; Sarantopoulos, Stefanie; Shea, Thomas C.; Serody, Jonathan S.; Alatrash, Gheath; Rodriguez-Cruz, Tania; Lizée, Gregory; Buntzman, Adam S.; Frelinger, Jeffrey A.; Glish, Gary L.; Armistead, Paul M.

doi:10.1158/2326-6066.22538669.v1

Supplementary Tables 1 - 4, Figures 1 - 2 from Peptide/MHC Tetramer–Based Sorting of CD8⁺ T Cells to a Leukemia Antigen Yields Clonotypes Drawn Nonspecifically from an Underlying Restricted Repertoire

journal contribution

posted on 2023-04-03, 23:11 authored by Sally A. Hunsucker, Colleen S. McGary, Benjamin G. Vincent, Atim A. Enyenihi, Jennifer P. Waugh, Karen P. McKinnon, Lisa M. Bixby, Patricia A. Ropp, James M. Coghill, William A. Wood, Don A. Gabriel, Stefanie Sarantopoulos, Thomas C. Shea, Jonathan S. Serody, Gheath Alatrash, Tania Rodriguez-Cruz, Gregory Lizée, Adam S. Buntzman, Jeffrey A. Frelinger, Gary L. Glish, Paul M. Armistead

The document contains 4 supplemental tables: 1. RT-PCR Primers for TCRbeta sequencing 2. HPLC-MS identified peptide sequences 3. The amino acid sequences of recurrent TCRbeta clonotypes 4. The distribution of the CDR3 amino acid length in the analyzed patient. There are 2 supplementary figures: 1. Tetramer flow cytometry showing the generation of an oligoclonal T-cell population with a UNC-CDK4-1 high affinity T-cell population. 2. More detailed information regarding the tetramer gating strategy employed.

History

ARTICLE ABSTRACT

Testing of T cell–based cancer therapeutics often involves measuring cancer antigen–specific T-cell populations with the assumption that they arise from in vivo clonal expansion. This analysis, using peptide/MHC tetramers, is often ambiguous. From a leukemia cell line, we identified a CDK4-derived peptide epitope, UNC-CDK4-1 (ALTPVVVTL), that bound HLA-A*02:01 with high affinity and could induce CD8+ T-cell responses in vitro. We identified UNC-CDK4-1/HLA-A*02:01 tetramer+ populations in 3 of 6 patients with acute myeloid leukemia who had undergone allogeneic stem cell transplantation. Using tetramer-based, single-cell sorting and T-cell receptor β (TCRβ) sequencing, we identified recurrent UNC-CDK4-1 tetramer–associated TCRβ clonotypes in a patient with a UNC-CDK4-1 tetramer+ population, suggesting in vivo T-cell expansion to UNC-CDK4-1. In parallel, we measured the patient's TCRβ repertoire and found it to be highly restricted/oligoclonal. The UNC-CDK4-1 tetramer–associated TCRβ clonotypes represented >17% of the entire TCRβ repertoire—far in excess of the UNC-CDK4-1 tetramer+ frequency—indicating that the recurrent TCRβ clonotypes identified from UNC-CDK-4-1 tetramer+ cells were likely a consequence of the extremely constrained T-cell repertoire in the patient and not in vivo UNC-CDK4-1–driven clonal T-cell expansion. Mapping recurrent TCRβ clonotype sequences onto TCRβ repertoires can help confirm or refute antigen-specific T-cell expansion in vivo. Cancer Immunol Res; 3(3); 228–35. ©2015 AACR.

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Keywords

Hematological Cancers Leukemias Immunology Graft versus host disease Immune responses to cancer Tumor antigens/neoantigens Immunotherapy

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