Abstract PO4-02-01: Characterization of immune and malignant cell evolution upon treatment pressure with aromatase inhibitors in locally advanced estrogen positive breast cancer

Abstract Background Aromatase inhibitors (AIs) are commonly used in the management of estrogen receptor-positive (ER+) breast cancer, as they effectively reduce estrogen levels which inhibits tumor growth and recurrence. In postmenopausal women with ER+ breast cancer, aromatase inhibitors are increasingly used in selected patients as neoadjuvant therapy to reduce the tumor burden before surgery and to improve overall treatment outcomes. Clinical trial The NEOLETEXE trial aimed to treat postmenopausal patients with locally advanced breast cancer. It was a neoadjuvant, randomized, open-label, intra-patient, cross-over, single-center phase II clinical trial. Most patients presented large T3/T4 tumors and/or N2/N3 involvement. Patients were randomly assigned to receive neoadjuvant therapy with either letrozole (2.5 mg daily) or exemestane (25 mg daily) for 3 months followed by a cross-over to the alternative AI for another 3 months followed by surgery. A total of 102 patients were enrolled in the NEOLETEXE trial. Aim of the study We aim at using single-cell analyses at different time points of treatment, to characterize evolutionary trajectories of cancer and immune cells in 23 patients from the NEOLETEXE trial. Methods Tumor biopsies taken before treatment (baseline) at crossover (after 3 months) and end of neoadjuvant therapy (after 6 months), were analyzed by single-cell RNA (scRNA), T cell receptor (TCR), and B cell receptor (BCR) sequencing. The data were first processed using cellRanger and the Seurat package. Results The main cell types found in tumors were identified through clustering of the scRNA data. We then focused on the epithelial cells to first distinguish between the normal and malignant epithelial cells using the InferCNV algorithm. For each patient, the analysis of inferred copy number events allowed to elucidate the genetic background of clones resistant or sensitive to aromatase inhibitors. This analysis unveiled the evolutionary dynamics of tumor heterogeneity during treatment. We next examined CD4, CD8, NK cells, and macrophages, using RNA velocity and diffusion pseudotime using CellRank and scVelo to delineate the differentiation trajectories of immune cell types. Conclusions We created a detailed map that provides a high-resolution view of the diverse cell types present in tumor biopsies from the NEOLETEXE trial. We characterize the impact of therapies on the evolutionary dynamics of both cancer and immune cells. Our analyzes sought insights into the underlying factors that contribute to the sensitivity and resistance to aromatase inhibitors. Citation Format: Leonard Schmiester, Salim Ghannoum, Marie Fongård, Marius Bjørnstad, Knut Selsås, Stephanie Geisler, Manouchehr Seyedzadeh, Unn-Cathrin Buvarp, Torben Lüders, Diether Lambrechts, Marianne Lyngra, Arnoldo Frigessi, Vessela Kristensen, Jürgen Geisler, Xavier Tekpli. Characterization of immune and malignant cell evolution upon treatment pressure with aromatase inhibitors in locally advanced estrogen positive breast cancer abstract. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-02-01.