299P - Single-cell transcriptomic analysis reveals specific luminal and T cell subpopulations associated with response to neoadjuvant therapy in early-stage breast cancer

Background

Neoadjuvant therapy (NAT) remains the standard of care for most early-stage breast cancer (BC) patients, especially in HER2+ and triple-negative (TNBC) subtypes. Patients who do not achieve pathological complete response (pCR) present an increased risk of disease recurrence. Here, we applied single cell RNA sequencing (SCS) to investigate tumor and immune landscape for the identification of predictive biomarkers of response to NAT.

Methods

Twenty-one BC patients treated with NAT were included in the study. Pre-treatment biopsies, matched residual disease and adjacent normal tissue samples were prospectively collected for all patients. After tissue dissociation, single cell RNA profiles were investigated using the Chromium Next GEM Single Cell 5' kit (10X Genomics). After removing batch effect using Seurat integration, cell clusters were annotated based on the expression of specific marker genes. Epithelial luminal cells (KRT18+/KRT19+) were classified as malignant or non-malignant using copy number profiles computed by inferCNV. Wilcoxon rank sum test was used to compare cell proportions between pCR and non-pCR groups.

Results

pCR rates were 61.5% (8/13), 100% (4/4) and 25% (1/4) in TNBC, HER2+ and Luminal B patients respectively. A total of 21 TNBC, 6 HER2+ and 6 Luminal B samples were profiled with SCS. Malignant luminal epithelial cells were classified in luminal progenitor (LP) (KIT+/SLPI+/KRT5^low), luminal mature (LM) (KIT-/SLPI-/KRT5-) and luminal cycling cells (LC) (MKI67+/TOP2A+). Patients achieving pCR had a higher fraction of LC cells at baseline, considering all BC subtypes (p<0.05). Enrichment of LP cells at baseline was observed in TNBC patients achieving pCR (p<0.05). T cells reclustering further identified four CD4+ subtypes. Of note, lower proportions of FOXP3+ regulatory T cells and RORC+/CCR6+ Th17 cells at baseline were associated with a better response to NAT both in TNBC and HER2+ patients (p<0.05).

Conclusions

Our study showed substantial heterogeneity at the single cell level with specific cell types being associated with response to neoadjuvant chemotherapy, towards an improved BC care.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B).

Funding

Fond de la Recherche Scientifique (FNRS), Télévie, Association Jules Bordet, Breast Cancer Research Foundation (BCRF), Fondation contre le Cancer, Fondation de l’Université Libre de Bruxelles.

Disclosure

C. Sotiriou: Financial Interests, Institutional, Advisory Board: Astellas, Vertex, Seattle Genetics, Amgen, INC, Merck & Co; Financial Interests, Personal, Advisory Board: Cepheid, Puma; Financial Interests, Personal, Invited Speaker: Eisai, Prime oncology, Teva; Financial Interests, Institutional, Other, Travel: Roche; Financial Interests, Institutional, Other, Internal speaker: Genentech; Financial Interests, Personal, Other, Regional speaker: Pfizer; Financial Interests, Institutional, Invited Speaker: Exact Sciences. All other authors have declared no conflicts of interest.