Self-supervised learning for characterising histomorphological diversity and spatial RNA expression prediction across 23 human tissue types

Francesco Cisternino, Sara Ometto, Soumick Chatterjee, Edoardo Giacopuzzi, Adam P. Levine and Craig A. Glastonbury ()
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Francesco Cisternino: Human Technopole
Sara Ometto: Human Technopole
Soumick Chatterjee: Human Technopole
Edoardo Giacopuzzi: Human Technopole
Adam P. Levine: University College London
Craig A. Glastonbury: Human Technopole

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: Abstract As vast histological archives are digitised, there is a pressing need to be able to associate specific tissue substructures and incident pathology to disease outcomes without arduous annotation. Here, we learn self-supervised representations using a Vision Transformer, trained on 1.7 M histology images across 23 healthy tissues in 838 donors from the Genotype Tissue Expression consortium (GTEx). Using these representations, we can automatically segment tissues into their constituent tissue substructures and pathology proportions across thousands of whole slide images, outperforming other self-supervised methods (43% increase in silhouette score). Additionally, we can detect and quantify histological pathologies present, such as arterial calcification (AUROC = 0.93) and identify missing calcification diagnoses. Finally, to link gene expression to tissue morphology, we introduce RNAPath, a set of models trained on 23 tissue types that can predict and spatially localise individual RNA expression levels directly from H&E histology (mean genes significantly regressed = 5156, FDR 1%). We validate RNAPath spatial predictions with matched ground truth immunohistochemistry for several well characterised control genes, recapitulating their known spatial specificity. Together, these results demonstrate how self-supervised machine learning when applied to vast histological archives allows researchers to answer questions about tissue pathology, its spatial organisation and the interplay between morphological tissue variability and gene expression.

Date: 2024
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DOI: 10.1038/s41467-024-50317-w

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