MRI-Based Deep Learning Guides Multi-Omics Discovery of NBPF4 as a Therapeutic Target for Breast Cancer Lymph Node Metastasis

Abstract

Deep learning models are increasingly used to analyze medical images, but their “black box” nature makes it hard to understand the underlying biology and slows down the development of targeted treatments. To tackle this, we built a multi-step approach that combines deep learning analysis of breast magnetic resonance imaging (MRI) with several types of molecular data, including gene activity, protein levels, and genetic information, along with laboratory experiments. Our MRI-based deep learning model accurately predicted whether breast cancer had spread to lymph nodes, and it performed consistently across 3 separate groups of patients. Causal inference using double least absolute shrinkage and selection operator (LASSO) and causal forest double machine learning established a significant effect of NBPF4 expression on the imaging-defined high-risk phenotype, independent of genomic confounders. When we looked at which genes were linked to the imaging-defined high-risk pattern, one gene called NBPF4 stood out because it was supported by all 4 kinds of evidence: imaging features, gene expression, protein data, and genetic association studies. Follow-up experiments in cells and animals showed that boosting NBPF4 activity made tumor cells grow faster, move more, form new lymphatic vessels, and spread to lymph nodes. Mechanistically, NBPF4 worked by activating the mitogen-activated protein kinase (MAPK) signaling pathway and triggering a process known as epithelial mesenchymal transition (EMT). Interestingly, tumors with high NBPF4 were sensitive to drugs that block one part of the MAPK pathway (JNK/p38) but resistant to another part (ERK), suggesting that the pathway had been rewired. Using this insight, computer-based drug screening and further testing identified MK-886 as a promising compound that could suppress NBPF4-promoted MAPK activation and tumor growth. Together, this work traces a complete path from a noninvasive imaging finding to a specific gene (NBPF4) and a potential treatment (MK-886). It establishes the NBPF4–MAPK–EMT axis as a key player in breast cancer metastasis and provides a general framework for turning imaging-based risk predictions into biological understanding and possible therapies.