Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy

Cancer Immunol Res. 2016 Oct;4(10):835-844. doi: 10.1158/2326-6066.CIR-16-0013. Epub 2016 Sep 1.

Abstract

In early-stage breast cancer, the degree of tumor-infiltrating lymphocytes (TIL) predicts response to chemotherapy and overall survival. Combination immunotherapy with immune checkpoint antibody plus tumor cryoablation can induce lymphocytic infiltrates and improve survival in mice. We used T-cell receptor (TCR) DNA sequencing to evaluate both the effect of cryoimmunotherapy in humans and the feasibility of TCR sequencing in early-stage breast cancer. In a pilot clinical trial, 18 women with early-stage breast cancer were treated preoperatively with cryoablation, single-dose anti-CTLA-4 (ipilimumab), or cryoablation + ipilimumab. TCRs within serially collected peripheral blood and tumor tissue were sequenced. In baseline tumor tissues, T-cell density as measured by TCR sequencing correlated with TIL scores obtained by hematoxylin and eosin (H&E) staining. However, tumors with little or no lymphocytes by H&E contained up to 3.6 × 106 TCR DNA sequences, highlighting the sensitivity of the ImmunoSEQ platform. In this dataset, ipilimumab increased intratumoral T-cell density over time, whereas cryoablation ± ipilimumab diversified and remodeled the intratumoral T-cell clonal repertoire. Compared with monotherapy, cryoablation plus ipilimumab was associated with numerically greater numbers of peripheral blood and intratumoral T-cell clones expanding robustly following therapy. In conclusion, TCR sequencing correlates with H&E lymphocyte scoring and provides additional information on clonal diversity. These findings support further study of the use of TCR sequencing as a biomarker for T-cell responses to therapy and for the study of cryoimmunotherapy in early-stage breast cancer. Cancer Immunol Res; 4(10); 835-44. ©2016 AACR.

Publication types

  • Controlled Clinical Trial

MeSH terms

  • Antineoplastic Agents, Immunological / therapeutic use
  • Biomarkers, Tumor / genetics*
  • Biopsy
  • Breast Neoplasms / genetics
  • Breast Neoplasms / immunology*
  • Breast Neoplasms / pathology
  • Breast Neoplasms / therapy
  • Combined Modality Therapy
  • Cryosurgery
  • DNA, Neoplasm / genetics
  • Feasibility Studies
  • Female
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Immunotherapy / methods*
  • Ipilimumab / therapeutic use
  • Leukemic Infiltration
  • Lymphocyte Count
  • Lymphocytes, Tumor-Infiltrating / immunology*
  • Mastectomy / methods
  • Neoplasm Staging
  • Pilot Projects
  • Receptors, Antigen, T-Cell, alpha-beta / genetics*
  • Receptors, Antigen, T-Cell, alpha-beta / immunology
  • Sequence Analysis, DNA / methods

Substances

  • Antineoplastic Agents, Immunological
  • Biomarkers, Tumor
  • DNA, Neoplasm
  • Ipilimumab
  • Receptors, Antigen, T-Cell, alpha-beta