A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

Abstract

Immune-checkpoint blockade (ICB) combined with neoadjuvant chemotherapy improves pathological complete response in breast cancer (BC). To understand why only a subset of tumors respond to ICB, patients with hormone receptor-positive or triple-negative BC were treated with anti-PD1 prior to surgery. Paired pre-versus on-treatment biopsies from treatment-naïve patients receiving anti-PD-1 (n=29) or patients receiving neoadjuvant chemotherapy prior to anti-PD1 (n=11) were subjected to single-cell transcriptome, T-cell receptor and proteome profiling. One-third of tumors contained PD1-expressing T-cells, which clonally expanded upon anti-PD1 treatment irrespective of tumor subtype. Expansion mainly involved CD8 + T-cells with pronounced expression of cytotoxic-activity (PRF1, GZMB), immune-cell homing (CXCL13) and exhaustion markers (HAVCR2, LAG3), and CD4 + T-cells characterized by expression of T-helper-1 (IFNG) and follicular-helper (BCL6, CXCR5) markers. In pre-treatment biopsies, the relative frequency of immunoregulatory dendritic cells (PD-L1), specific macrophage phenotypes (CCR2 or MMP9) and cancer cells exhibiting MHC class I/II expression correlated positively with T-cell expansion. Conversely, undifferentiated preeffector/memory T-cells (TCF7, GZMK) or inhibitory macrophages (CXCR3, C3) were inversely correlated. Collectively, our data identify various immunophenotypes and associated gene sets that are positively or negatively correlated with T-cell expansion following anti-PD1. We shed light on the heterogeneity in treatment response to anti-PD1 in breast cancer.

Intra-Tumour Heterogeneity Is One of the Main Sources of Inter-Observer Variation in Scoring Stromal Tumour Infiltrating Lymphocytes in Triple Negative Breast Cancer

“…Furthermore, recent trial data suggest that pre-and on-treatment sTILs can have a role in the selection of patients for immune check point blocking therapies [37]. The number of lymphocytes seems to increase after only one dose of immune therapy and is associated with significant clonotype changes in T cells suggesting activation of T cells based on the expression of immune-check point, effector, and cytotoxic markers [38].…”

Clinical Trials with Biologic Primary Endpoints in Immuno-oncology: Concepts and Usage

“…A recent window of opportunity trial in HER2-breast cancer (NCT03197389) utilized single cell RNA seq, TCR seq and CITE-seq to evaluate immune cell populations before and after neoadjuvant pembrolizumab. 47 This approach demonstrated on-treatment clonal expansion of T cells within specific T cell subsets. Additional immune cell subsets including dendritic cells and macrophages were quantified and correlated with T cell expansion.…”

The Comprehensive “Omics” Approach from Metabolomics to Advanced Omics for Development of Immune Checkpoint Inhibitors: Potential Strategies for Next Generation of Cancer Immunotherapy

“…Bassez et al analyzed clinical samples from breast cancer patients who received only anti-PD1 or neoadjuvant chemotherapy before anti-PD1 using single-cell transcriptomics combined with proteome profiling to understand a subset of tumors responding to ICI. This study identified the association of T-cell expansion after anti-PD1 treatment with immunophenotypes and gene sets positively (e.g., expression of PRF1, GZMB, and CXCL13) or negatively (e.g., TCF7+, GZMK+ T-cells, and CX3CR1+, C3+ inhibitory macrophages) [146]. Sade-Feldman et al applied single-cell RNA sequencing to profile transcriptomes of more than 16,000 individual immune cells derived from 48 patients with melanoma in a discovery set.…”