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To bypass the high cost and turnaround time of whole-genome sequencing for precision oncology, the authors developed Hist2Sig to predict exposures across 30 COSMIC single-base substitution (SBS) mutational signatures directly from routine H&E whole slide images. Evaluated across 7,063 TCGA patients spanning 29 cancer types, the framework outperformed tissue-of-origin prior baselines in top-three signature overlap across 19 indications—with pronounced gains in colorectal, prostate, glioblastoma, and uterine cancers—while maintaining moderate external generalization on a 193-patient CPTAC cohort. Crucially, the model successfully recovered complex signatures of both established clinical utility (such as MMR and HRD) and poorly understood etiologies (including SBS8, SBS12, and SBS40a), demonstrating that routine morphological features track systemic genomic instability.
Standard cancer histology encodes enough latent signal to reconstruct genome-wide mutational signature distributions without sequencing, consistently beating tissue-of-origin priors across 19 distinct malignancies.
Mutational signatures reveal cancer-driving processes with clinical relevance: MMR-deficient tumors respond better to immunotherapy, HRD tumors are sensitive to PARP inhibitors, and POLE-mutant tumors often have high mutation burdens influencing treatment response. Yet signature profiling remains limited by the cost, complexity, and turnaround time of whole-genome sequencing (WGS) or whole-exome sequencing. Histopathology is widely available and cost-effective, and H&E morphology has been linked to MSI, HRD, POLE-related processes, and driver mutations. Whether histology can recover the broader landscape of mutational signature exposures in a pan-cancer setting remains unknown. Here we introduce Hist2Sig, a deep learning framework predicting exposures to 30 COSMIC SBS signatures from H&E-stained slides. Trained on matched WGS and histology data from 7,063 TCGA patients across 29 cancer types, Hist2Sig was compared with a tumor type-only baseline to separate morphology-derived signal from tissue-of-origin priors. In internal cross-validation, it recovered relative signature compositions across most tumor types and achieved higher mean top-three overlap than the baseline in 19 of 29, with the largest gains in COAD, PRAD, GBM, and UCEC. It also recurrently recovered signatures of poorly characterized etiology, including SBS8, SBS12, SBS39, and SBS40a. In an external CPTAC cohort of 193 patients across five tumor types, Hist2Sig retained moderate concordance with observed compositions and outperformed the baseline in glioblastoma and pancreatic adenocarcinoma. These results support the feasibility of inferring mutational signature exposures from routine histology, while highlighting variation across tumor types. Hist2Sig provides a foundation for tumor-specific models that could complement sequencing in pre-sequencing triage or support decisions where WGS is unavailable.