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

Abstract

In early stage breast cancer, the degree of tumor-infiltrating lymphocytes (TILs) 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 cryo-immunotherapy 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 to 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 cryo-immunotherapy in early-stage breast cancer.

Targeting immune checkpoints in breast cancer: an update of early results

“…Interestingly cryoablation +/− ipilimumab modelled the clonal repertoire of intratumoural T cells, with patients that received the combination approach demonstrating greater levels of peripheral blood and intratumoural T cell clones after therapy. 99 Some of the ongoing trials evaluating CTLA-4 blockade in combination with other ICB agents are listed in online supplementary table s1.…”

Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications—The Role of Molecular Dynamics Simulation

“…Generally, breast cancer is diagnosed by using various molecular tools to detect specific biomarkers such as estrogen‐related favorable and unfavorable α and γ receptors, σ receptors, androgen receptors, human epidermal growth factor, and progesterone receptors . In recent times, biomarkers such as T‐cell receptor DNA, tumor‐infiltrating lymphocytes, breast cancer type 1 susceptibility protein (BRCA1), and cyclin‐dependent kinase (CDK) 4/6 inhibitors are used for the detection and targeted treatment of breast cancer. Breast cancer specific biomarkers including non‐antibody proteins, monoclonal antibodies, and small molecule drugs are heralding recent target‐specific treatment methods used for effective cancer therapies …”

Beyond PD-L1 testing-emerging biomarkers for immunotherapy in non-small cell lung cancer

“…In another retrospective analysis of 46 patients with metastatic melanoma receiving pembrolizumab from KEYNOTE-001, sequencing of TCR beta chain CDR3 variable region in matched pre-and post-treatment tumor samples showed that responders had a ten-fold increase in expanded T cell clones compared with non-responders (17). Another small pilot study of ipilimumab, cryoablation, or both in 18 early stage breast cancer patients showed increase intratumoral T cells clones detected by TCR sequencing after ipilimumab +/− cryoablation (24).…”