Unveiling the Fusion Immune Atlas: A Unified Platform for Gene Fusion Data Integration

Strategic Insights -

Gene fusions play a pivotal role in cancer development by activating kinases or inactivating tumor suppressor genes, leading to altered signal transduction and gene expression regulation. However, their impact on treatment responses remains poorly understood. The lack of a unified platform integrating gene fusion data across cancer types, linking them to the tumor microenvironment (TME), and patient outcomes hinders the understanding of fusions' influence on immune responses and the development of personalized cancer therapies. To address this gap, researchers constructed the Fusion Immune Atlas (ImmunoFusion), a platform integrating data from TCGA, TARGET, CPTAC, and 29 ICB cohorts across diverse cancer types.

Key Takeaways:

  • The Fusion Immune Atlas (ImmunoFusion) is a unified platform integrating gene fusion data across cancer types, linking them to the tumor microenvironment (TME), and patient outcomes.
  • ImmunoFusion encompasses 21,014 clinical samples, serving as a comprehensive RNA-seq-derived gene fusion database and analytical tool.
  • The platform offers functionalities to investigate fusion breakpoints, confidence scores, frequency patterns, and associations with clinical variables.
  • ImmunoFusion enables TME evaluation and interactive exploration of fusions for analyzing tumor immunophenotypes in cancer and immunotherapy contexts.
  • Analysis of MTAP fusions in lung cancer cohorts revealed their association with a metabolically depleted, "cold" tumor environment and poorer patient outcomes, pinpointing MTAP fusions as a novel biomarker for treatment selection.
  • The platform's value lies in understanding fusion-driven immunotherapy outcomes, paving the way for more effective therapeutic strategies.

Statistics:

  • 21,014 clinical samples are included in ImmunoFusion.
  • The platform integrates data from TCGA, TARGET, CPTAC, and 29 ICB cohorts.
  • 29 ICB cohorts are used in the integration, including ICB treatments and other treatment modalities.
  • 21,014 clinical samples were used to develop ImmunoFusion.
  • The platform offers an interactive exploration of fusions for analyzing tumor immunophenotypes.

Sources:

  • biorxiv.org/content/10.1101/2025.06.05.658082v1
  • TCGA
  • TARGET
  • CPTAC
  • Immuno-Oncology Biological Research (IOBR) approach
  • STAR-Fusion
  • Arriba
  • MetaFusion
  • GRCh38 reference genome
  • Rhino framework for Shiny applications
  • R programming language