Abstract

Background Immune checkpoint blockade (ICB) therapy has provided a promising treatment option for patients with triple-negative breast cancer (TNBC). However, existing efficacy prediction strategies based on programmed death-ligand 1 (PD-L1) expression and Tumor Mutational Burden (TMB) have significant limitations, leading to inaccurate patient selection. Methods This study integrated multi-omics data obtained from GEO, TCGA, and GTEx datasets. Based on ComBat correction results, two deep learning-driven unsupervised clustering methods were constructed to identify potential immune subtypes. These identified TNBC subtypes were subjected to comprehensive bioinformatics analyses to investigate their differences in overall survival, immune cell infiltration, and functional enrichment analysis, which clarified the biological rationale of the proposed classification. Subsequently, differential expression analysis (DEA) and multiple machine learning algorithms were applied to identify subtype-specific features, with the expression and differentiation status of the key feature in immune cells further validated using single-cell sequencing (scRNA-seq). Finally, co-expression networks at multiple cellular levels were constructed to predict the co-expressed regulatory targets of the key feature, and the hypothesized regulatory mechanism was preliminarily validated in in vitro experiments (qRT-PCR, western blotting, immunofluorescence, and ELISA). Results After 5-fold cross-validation, the AE-K-means clustering method classified TNBC into three distinct latent subtypes. This algorithm exhibited superior classification efficacy compared with the other models (including NMF, ConsensusClusterPlus and VAE-GMM), as demonstrated by markedly elevated Silhouette Coefficients (training: 0.585 ± 0.030; test: 0.698 ± 0.103; validation: 0.611) and substantially reduced Davies-Bouldin Index values (training: 0.623 ± 0.032; test: 0.385 ± 0.218; validation: 0.558) at K = 3. These three ident