Single-cell and spatial transcriptome profiling identifies cellular heterogeneity and immunosuppressive tumor microenvironment in inflammatory breast cancer

Abstract

Introduction: Inflammatory breast cancer (IBC) is a highly aggressive subtype of breast cancer associated with a poor prognosis. A better understanding of IBC's pathological and molecular basis is crucial for developing precision medicine strategies.

Objective: This study aimed to profile IBC at both the single-cell and spatial levels to examine immune cell populations, signaling pathways, and identify potential therapeutic targets for treating IBC.

Methods: Single-cell RNA sequencing (scRNA-seq) was employed to identify immune-related differences between IBC and non-IBC samples. qRT-PCR and fluorescence staining were utilized to validate the findings from scRNA-seq, while spatial analysis using the NanoString GeoMx Digital Spatial Profiler was conducted to evaluate immune cell infiltration. Tumor-immune cell co-culture assays were conducted to assess the cytotoxic role of CXCL13. In vivo studies were performed to assess the effect of CXCL13 on the efficacy of immunotherapy. Furthermore, a screening of natural products was performed to identify potential immunomodulatory agents for the treatment of IBC.

Results: scRNA-seq revealed a significant reduction in CXCL13 expression in T cells within the IBC tumor microenvironment, a finding that correlated with poorer patient outcomes. Additionally, immune-related gene sets were notably downregulated, and cell-cell interactions were diminished, indicating a state of immune suppression within IBC. Spatial analysis further demonstrated a reduced presence of CD45-positive immune cells within IBC tumor tissues, highlighting the compromised immune infiltration characteristic of this aggressive cancer subtype. Most importantly, overexpression of CXCL13 in tumor cells, under co-culture with immune cells, significantly promoted tumor cell death. CXCL13 can also enhance the efficacy of anti-PD-1 therapy in vivo. Furthermore, screening of natural products identified sanguinarine and α-mangostin as potential immunomodulatory compounds, offering promising therapeutic avenues for modulating the immune response in IBC and improving treatment outcomes.

Conclusion: Our findings reveal inherent heterogeneity within the "cold" tumor microenvironment of IBC. These factors collectively contribute to the immune suppression characteristic of IBC. Additionally, natural product screening identified sanguinarine and α-mangostin as promising immunomodulatory agents, offering potential therapeutic strategies to improve treatment outcomes.

Keywords: Immune response; Inflammatory breast cancer; Natural products; Single cell RNA sequencing; Tumor microenvironment.