BRIDGE: A Multi-organ Histo-ST Foundation Model Enables Virtual Spatial Transcriptomics for Enhanced Few-shot Cancer Diagnosis

Abstract

Recent studies have explored generating virtual spatial transcriptomics (ST) profiles from histological images, offering a promising alternative to laboratory-measured molecular profiling. However, existing approaches predominantly rely on single-organ models and require sub-stantial organ-specific training data, restricting their accuracy under challenging few-shot conditions in clincical practice, where less than 10 slides are available for specific organs or techniques. Here, we present BRIDGE, a multi-organ foundation model pre-trained on over 600,000 paired histology-ST profiles across 13 human organs and three sequencing techniques. By robustly aligning morphological features and genomic information within a shared multi-organ latent space, BRIDGE can leverage common biological knowledge across distinct tissues to enable accurate and generalizable pan-cancer molecular profiling. Without additional organ-specific fine-tuning, BRIDGE accurately predicts the spatial expression of 80 biomarker genes, achieving an average Pearson correlation coefficient (PCC) of 0.474--a 30% improvement over existing state-of-the-art models under three clinically challenging few-shot scenarios. With generated virtual ST, BRIDGE outperforms current state-of-the-art pathology foundation models in predicting cancer survival, achieving an average concordance index (C-index) of 0.724 across six TCGA cohorts. Notably, BRIDGE maintains exceptional performance even in zero-shot scenarios involving three cancer types not seen during its training, achieving an average C-index of 0.717, thereby demonstrating its strong generalization capability that transcends organ- and subtype-specific boundaries. Moreover, BRIDGE-generated virtual spatial transcriptomes match the prognostic accuracy of bulk RNA-seq, highlighting their potential as a spatially informative alternative to laboratory sequencing. In general, BRIDGE represents a data-efficient tool in virtual ST that facilitates biomedical discoveries in clinical few-shot contexts and advances diagnosis of understudied cancers without sufficient samples.