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

• Published in: Cancer immunology research 2016-10, Vol.4 (10), p.835-844
• Main Authors: Page, David B, Yuan, Jianda, Redmond, David, Wen, Y Hanna, Durack, Jeremy C, Emerson, Ryan, Solomon, Stephen, Dong, Zhiwan, Wong, Phillip, Comstock, Christopher, Diab, Adi, Sung, Janice, Maybody, Majid, Morris, Elizabeth, Brogi, Edi, Morrow, Monica, Sacchini, Virgilio, Elemento, Olivier, Robins, Harlan, Patil, Sujata, Allison, James P, Wolchok, Jedd D, Hudis, Clifford, Norton, Larry, McArthur, Heather L
• Format: Article
• Language: English
• Subjects: 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
• ISSN: 2326-6066; 2326-6074
• DOI: 10.1158/2326-6066.CIR-16-0013

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 × 10 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.