Integrating single‐cell transcriptomics and machine learning to predict breast cancer prognosis: A study based on natural killer cell‐related genes

Abstract

AbstractBreast cancer (BC) is the most commonly diagnosed cancer in women globally. Natural killer (NK) cells play a vital role in tumour immunosurveillance. This study aimed to establish a prognostic model using NK cell‐related genes (NKRGs) by integrating single‐cell transcriptomic data with machine learning. We identified 44 significantly expressed NKRGs involved in cytokine and T cell‐related functions. Using 101 machine learning algorithms, the Lasso + RSF model showed the highest predictive accuracy with nine key NKRGs. We explored cell‐to‐cell communication using CellChat, assessed immune‐related pathways and tumour microenvironment with gene set variation analysis and ssGSEA, and observed immune components by HE staining. Additionally, drug activity predictions identified potential therapies, and gene expression validation through immunohistochemistry and RNA‐seq confirmed the clinical applicability of NKRGs. The nomogram showed high concordance between predicted and actual survival, linking higher tumour purity and risk scores to a reduced immune score. This NKRG‐based model offers a novel approach for risk assessment and personalized treatment in BC, enhancing the potential of precision medicine.