Novel multi-omics analysis revealing metabolic heterogeneity of breast cancer cell and subsequent development of associated prognostic signature

Abstract

Background

Breast cancer remains one of the most prevalent malignancies globally, with metabolic reprogramming contributing significantly to tumor progression, immune evasion, and treatment resistance. Understanding the metabolic heterogeneity and its interaction with the tumor microenvironment is crucial for improving prognostic predictions and therapeutic strategies.

Methods

We integrated single-cell RNA sequencing (scRNA-seq), bulk RNA sequencing, and clinical data to characterize metabolic patterns in breast cancer. Immunoregulatory genes were obtained from the TISIDB database and analyzed by weighted gene co-expression network analysis (WGCNA) to identify key metabolic-related modules and hub genes. A metabolic risk signature was constructed using machine learning algorithms. Immune cell infiltration and immune checkpoint profiles were assessed to explore tumor microenvironment differences. Drug sensitivity prediction was performed via the OncoPredict tool. Functional assays investigated the oncogenic role of PDCD1 in breast cancer cell lines.

Results

We identified distinct breast cancer epithelial subpopulations with highly activated glycolysis and associated metabolic pathways. Two patient clusters showed significant prognostic differences; the cluster with elevated glycolytic activity exhibited increased immune suppression, higher M2 macrophage infiltration, and poorer survival outcomes. The metabolic risk signature demonstrated robust prognostic power across multiple cohorts. High-risk patients displayed increased immune suppressive markers and reduced chemotherapy sensitivity. PDCD1 knockdown experiments confirmed its role in promoting proliferation, migration, and invasion of breast cancer cells.

Conclusions

Our study reveals metabolic heterogeneity linked to glycolytic reprogramming and immune modulation in breast cancer. The established metabolic signature offers a powerful prognostic tool and identifies potential therapeutic targets such as PDCD1. These findings contribute to precision oncology by guiding tailored treatment strategies based on metabolic and immune profiles.