HistoAtlas: A Pan-Cancer Morphology Atlas Linking Histomics to Molecular Programs and Clinical Outcomes

TL;DR

HistoAtlas is a comprehensive pan-cancer atlas linking histomic features from routine H&E slides to molecular and clinical data, enabling large-scale biomarker discovery without specialized tests.

Contribution

It introduces a systematic approach to extract and analyze histomic features across multiple cancer types, linking them to molecular and clinical outcomes.

Findings

Recovers known biological signals such as immune infiltration and proliferation.

Uncovers new compartment-specific immune signals and morphological subtypes.

Provides an open, spatially traceable, and statistically calibrated resource for biomarker discovery.

Abstract

We present HistoAtlas, a pan-cancer computational atlas that extracts 38 interpretable histomic features from 6,745 diagnostic H&E slides across 21 TCGA cancer types and systematically links every feature to survival, gene expression, somatic mutations, and immune subtypes. All associations are covariate-adjusted, multiple-testing corrected, and classified into evidence-strength tiers. The atlas recovers known biology, from immune infiltration and prognosis to proliferation and kinase signaling, while uncovering compartment-specific immune signals and morphological subtypes with divergent outcomes. Every result is spatially traceable to tissue compartments and individual cells, statistically calibrated, and openly queryable. HistoAtlas enables systematic, large-scale biomarker discovery from routine H&E without specialized staining or sequencing. Data and an interactive web atlas are freely available at https://histoatlas.com .