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Updated: Jan 23, 2026

A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis
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The GF-NEO discovery platform unveils a [KQE][DG] sequence motif within fusion neoantigens in pediatric cancer

Christopher Savoie1, Zhaoguan Wu1, Frederic Saab1

  • 1Centre de recherche de l'Hôpital Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada.

Iscience
|January 22, 2026
PubMed

Insights

This study introduces ProteoFusioNEO, a tool to identify fusion protein neoantigens in pediatric cancers. These neoantigens show promise for developing targeted immunotherapies against childhood cancers.

Area of Science:

  • Oncology
  • Bioinformatics
  • Immunotherapy

Background:

  • Gene fusions (GFs) are key drivers in pediatric cancers, but their fusion proteins and derived neoantigens (GF-NEOs) are understudied for immunotherapy.
  • Targeted immunotherapy approaches for pediatric oncology need further exploration of GF-NEOs.

Purpose of the Study:

  • To develop and validate a computational tool, ProteoFusioNEO, for identifying GF-NEOs from transcriptomic data.
  • To analyze the characteristics and presentation of GF-NEOs in pediatric cancer patients and cell lines.

Main Methods:

  • Developed ProteoFusioNEO for in silico translation of transcriptomic data from 5,190 pediatric cancer patients and 935 cell lines.
  • Analyzed fusion protein characteristics, including translational outcomes and sequence motifs at fusion junctions.
  • Validated GF-NEOs presentation using in vitro and in vivo systems, mass spectrometry, proteomics, and immunopeptidomics.

Main Results:

  • Identified 382 fusion proteins in patients and 446 in cell lines, with 97% being in-frame.
  • Discovered a conserved sequence motif [KQE][DG] at fusion junctions, potentially influencing GF-NEOs abundance.
  • Confirmed the presentation of multiple GF-NEOs, including those from ETV6-RUNX1 fusions, via experimental validation.

Conclusions:

  • ProteoFusioNEO effectively identifies fusion proteins and GF-NEOs from transcriptomic data.
  • GF-NEOs have distinct characteristics and can be experimentally validated, offering new targets for pediatric cancer immunotherapy.
  • This work lays the foundation for developing novel targeted immunotherapies based on GF-NEOs.
Keywords:
Biological sciences toolsCancerIn silico biologyOmics

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