Network-Based Clustering Unveils Interconnected Landscapes of Genomic and Clinical Features Across Myeloid Malignancies

Authors

Fritz Bayer
Marco Roncador
Giusi Moffa
Kiyomi Morita
Koichi Takahashi
Niko Beerenwinkel
Jack Kuipers

Publication Date

4-30-2025

Journal

Nature Communications

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.

Keywords

Humans, Mutation, Genomics, Prognosis, Cluster Analysis, Cohort Studies, Female, Male, Myeloproliferative Disorders

DOI

10.1038/s41467-025-59374-1

PMID

40301336

PMCID

PMC12041249

PubMedCentral® Posted Date

4-30-2025

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes