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The GF-NEO Discovery Platform: A Systems-Level Approach to Analyzing and Validating Fusion Neoantigens in Pediatric Cancer

ABSTRACT: Gene fusions (GFs) are critical events in pediatric oncology, often serving as oncogenic drivers. However, fusion proteins and their derived neoantigens (GF-NEOs) remain underexplored for targeted immunotherapy. We developed ProteoFusioNEO, a computational tool for in silico translation of transcriptomic data, analyzing 5,190 pediatric cancer patients and 935 cell lines, yielding 382 and 446 fusion proteins. We highlight that GFs generate multiple translational outcomes with 97% being in-frame in patients. Fusion junctions exhibit the sequence motif [KQE][DG] which partly reflects the nature of exon–exon junctions albeit with additional hydrophilicity. Moreover, GF-NEOs abundance may be shaped by the motif, offering insights into fusion protein biology. Finally, a multipronged validation strategy using in vitro and in vivo systems confirms the GF-NEOs presentation through mass spectrometry-based proteomics and immunopeptidomics. Multiple GF-NEOs encoded by two versions of the ETV6-RUNX1 fusion were validated, paving the way for targeted immunotherapy development.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Lymphoblast, Cell, Blood

DISEASE(S): Leukemia,Cancer

SUBMITTER: Christopher Savoie

LAB HEAD: Isabelle Sirois

PROVIDER: PXD063253 | Pride | 2025-11-26

REPOSITORIES: Pride

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			Action	DRS
	01_06_2022_A8028_9_N1_06_05_2022_NUP98_KDM5A_AND_PROTEASOME.mzid	Mzid
	01_06_2022_A8028_9_N1_06_05_2022_NUP98_KDM5A_AND_PROTEASOME_R1.mgf	Mgf
	01_06_2022_A8028_9_N1_06_05_2022_NUP98_KDM5A_AND_PROTEASOME_R1.raw	Raw
	01_06_2022_A8028_9_N1_06_05_2022_NUP98_KDM5A_AND_PROTEASOME_R2.mgf	Mgf
	01_06_2022_A8028_9_N1_06_05_2022_NUP98_KDM5A_AND_PROTEASOME_R2.raw	Raw

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