Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies

Fritz Bayer, Marco Roncador, Giusi Moffa, Kiyomi Morita, Koichi Takahashi, Niko Beerenwinkel and Jack Kuipers ()
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Fritz Bayer: ETH Zurich
Marco Roncador: ETH Zurich
Giusi Moffa: University of Basel
Kiyomi Morita: The University of Texas MD Anderson Cancer Center
Koichi Takahashi: The University of Texas MD Anderson Cancer Center
Niko Beerenwinkel: ETH Zurich
Jack Kuipers: ETH Zurich

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Myeloid malignancies exhibit considerable heterogeneity with overlapping clinical and genetic features among subtypes. We present a data-driven approach that integrates mutational features and clinical covariates at diagnosis within networks of their probabilistic relationships, enabling the discovery of patient subgroups. A key strength is its ability to include presumed causal directions in the edges linking clinical and mutational features, and account for them aptly in the clustering. In a cohort of 1323 patients, we identify subgroups that outperform established risk classifications in prognostic accuracy. Our approach generalises well to unseen cohorts with classification based on our subgroups similarly offering advantages in predicting prognosis. Our findings suggest that mutational patterns are often shared across myeloid malignancies, with distinct subtypes potentially representing evolutionary stages en route to leukemia. With pancancer TCGA data, we observe that our modelling framework extends naturally to other cancer types while still offering improvements in subgroup discovery.

Date: 2025
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DOI: 10.1038/s41467-025-59374-1

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