Spatially guided translation from histology images to transcriptomic profiles using foundation model-driven contrastive learning

Abstract

Spatial transcriptomics (ST) enhances single-cell RNA sequencing by revealing transcript distribution, offering critical insights into heterogeneous diseases such as breast cancer. However, the high cost and lengthy processes of generating high-quality ST data limit clinical application. Recent deep learning methods predict ST from histology images, but often fail to capture both morphological features and spatial context. We introduce FOCST, a foundation model-driven framework for ST imputation that leverages spatial guided contrastive learning. FOCST begins with UNI, a large histopathology foundation model, to extract visual features from tissue images. These are integrated with expression data in a unified embedding space via contrastive learning, enabling cross-modal prediction and imputation. To further enhance spatial awareness, a graph neural network incorporates positional information, improving regional detection and interpretability.Benchmarking demonstrates FOCST’s superior performance over state-of-the-art methods and alternative vision encoders (paired Wilcoxon signed-rank tests, FDR-adjusted p < 0.05, N = 6 images). Predicted profiles enable clinically relevant downstream analyses, including patient stratification by treatment response (ROC AUC (Receiver Operating Characteristic – Area Under the Curve) = 0.79). Our results highlight the promise of combining foundation models and spatially guided learning to efficiently generate ST insights, advancing cancer research and precision medicine.