Pan-cancer analysis of patient-specific gene regulatory landscapes identifies recurrent PD-1 pathway dysregulation linked to outcome

Abstract

Cancer heterogeneity remains a major challenge to the development of broadly effective therapies. Although gene expression-based stratification has advanced our understanding of molecular subtypes, it often overlooks the regulatory mechanisms driving tumor progression and therapeutic resistance. These mechanisms are governed by gene regulatory networks--complex systems of transcription factors and other regulators that control gene expression. To investigate regulatory heterogeneity at the patient level, we inferred individual gene regulatory networks for over 9,000 tumors across 33 cancer types from The Cancer Genome Atlas enabling a comprehensive pancancer analysis of inter-patient regulatory variation. Our analysis uncovered novel regulatory subtypes and revealed recurrent dysregulation of the PD-1 signaling pathway in 23 cancer types. This dysregulation was associated with patient outcomes in 12 cancers and appeared largely independent of established molecular subtypes and immune cell composition, suggesting alternative regulatory mechanisms. We identified both well-characterized (FOS, JUNB, ATF3) and previously unrecognized (RFX7, ELF1, NFYA, NFYC) transcriptional regulators of PD-L1 (CD274), highlighting new candidate targets for modulating immune checkpoint activity across tumor types. Our work demonstrates the power of single-sample gene regulatory networks to uncover hidden layers of tumor biology, improve patient stratification, and inform future research in immunotherapy.