168382 20260204153543.0 doi 10.1016/j.isci.2025.113061 sideral 147831 ART-2025-147831 eng Yin, Liangwei Sample-specific network analysis identifies gene co-expression patterns of immunotherapy response in clear cell renal cell carcinoma 2025 Immunotherapies have recently emerged as a standard of care for advanced cancers, offering remarkable improvements in patient prognosis. However, only a small subset of patients benefit, and robust molecular predictors remain elusive. We present a computational framework leveraging sample-specific gene coexpression networks to identify features predictive of immunotherapy response in kidney cancer. Our results reveal that patients with similar clinical outcomes exhibit comparable gene co-expression patterns. Notably, increased gene connectivity and stronger negative gene-gene associations are hallmarks of poor responders. We further developed sample-specific pathway-level network scores to detect dysregulated biological pathways linked to treatment outcomes. Finally, incorporating these sample-level network features improves the predictive performance of gene expression-based machine learning models. This work highlights the value of personalized gene network features for stratifying patients with cancer and optimizing immunotherapy strategies. Access copy available to the general public Unrestricted info:eu-repo/grantAgreement/EC/H2020/101017453/EU/Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity/KATY This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No H2020 101017453-KATY info:eu-repo/semantics/openAccess by https://creativecommons.org/licenses/by/4.0/deed.es info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Traversa, Pietro Universidad de Zaragoza Elati, Mohamed Moreno, Yamir Universidad de Zaragoza (orcid)0000-0002-0895-1893 Marek-Trzonkowska, Natalia Battail, Christophe 2004 405 Universidad de Zaragoza Dpto. Física Teórica Área Física Teórica 28, 8 (2025), 113061 iScience ISCIENCE 2589-0042 Sample-specific network analysis identifies gene co-expression patterns of immunotherapy response in clear cell renal cell carcinoma https://zenodo.org/records/15723818 10527372 http://zaguan.unizar.es/record/168382/files/texto_completo.pdf Versión publicada 1286888 http://zaguan.unizar.es/record/168382/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:168382 articulos driver 2026-02-04-13:14:55 ARTICLE