Gene regulatory network integration with multi-omics data enhances survival predictions in cancer.

Abstract

The emergence of high-throughput omics technologies has resulted in their wide application to cancer studies, greatly increasing our understanding of the disruptions occurring at different molecular levels. To fully harness these data, integrative approaches have emerged as essential tools, enabling the combination of multiple omics modalities to uncover disease mechanisms. However, many such approaches overlook gene regulatory mechanisms, which play a central role in the development and progression of cancer. Patient-specific gene regulatory networks (GRNs), representing interactions between regulators (such as transcription factors) and their target genes in each individual tumour, offer a powerful framework to bridge this gap and investigate the regulatory landscape of cancer. In this study, we introduce a novel approach for integrating patient-specific GRNs with multi-omic data and assess whether their inclusion in joint dimensionality reduction models improves survival prediction across multiple cancer types. By applying our method on ten cancer datasets from The Cancer Genome Atlas, we demonstrate that incorporating GRNs enhances associations with patient survival in several cancer types. Focusing on liver cancer, with validation in independent data, our methodology identifies potential mechanisms of gene regulatory dysregulation associated with cancer progression. These were linked to dysregulated fatty acid metabolism, and identified JUND as a potential novel transcriptional regulator driving these processes. Our findings highlight the value of network-based multi-omics integration for uncovering clinically relevant regulatory mechanisms and improving our understanding of cancer biology at the patient-specific level.