EXPLORE-NB

Background: Effective high-risk neuroblastoma treatment is an unmet medical need. Half the cases relapse, with <20% survival. Recent studies identified epigenetic mechanisms mediating phenotypic neuroblastoma heterogeneity and contributing to tumor evolution and resistance development. Cell-free DNA (cfDNA) contains nucleosome protein-DNA complexes cleaved from chromosomal DNA, opening liquid biopsies to epigenetic exploration. Epigenetic mechanisms in the tumorigenic microenvironment have so far remained largely unknown.
Hypothesis & aims: We hypothesize comprehensive epigenomic profiling in liquid biopsies can decipher the continuously evolving epigenetic landscape of metastasized neuroblastoma. EXPLORE-NB aims to identify and validate predictive epigenetic markers for treatment response, minimal residual disease (MRD) and relapse in liquid biopsies. Secondary aims explore the affected tissue microenvironment (tumor/metastases) to advance unique epigenetic-based innovations for patient monitoring and personalized treatment.
Methods: The interdisciplinary team assembled in EXPLORE-NB will apply ChIP-seq, scRNA-seq, scATAC-seq, spatial transcriptomics & single-molecule long-read-seq within 6 structured WPs, each focused to study cfDNA chromatin structure & DNA methylation in a different liquid biopsy component (WP1-2,4-6) or epigenetic rewiring through interactions with nontumor cells at primary and metastatic tumor sites (WP2-3,6). Direct SIOPEN clinical trial group participation in EXPLORE-NB assures partners use the same serially collected blood plasma, bone marrow, urine & cerebrospinal fluid samples (+matched primary/relapsed tumor, germline samples) from 400 uniformly treated patients with complete follow-up data and provides the prospective sample series (SIOPEN HR-NBL2 trial). Patient imaging data will corroborate conclusions from epigenetic biomarker discovery. Technically validated epigenetic biomarkers will be prospectively assessed in the SIOPEN HR-NBL2 co-clinical trial.
Expected results & potential impact: We expect to identify epigenetic mechanisms involved in treatment escape (tumor cell state switching,WP1). An assay to diagnose/monitor epigenetic immunosuppression and tumor promotion in the metastatic bone marrow niche will be developed (WP2). Spatially localized effects of induction polychemotherapy on neuroblastoma and stromal cells in the primary tumor will be elucidated with our novel in-house spatial transcriptomics platform (WP3). The power of cfDNA to spatially (metastatic invasion) and temporally resolve epigenetic disease evolution (genome-wide differentially hydroxymethylated/methylated regions combined with sequence) will be explored in cfDNA from biofluid sample series matched to tumor samples (WP4-6). We expect to generate technically and prospectively validated epigenetic markers/assays for treatment response, MRD and relapse to improve personalized care of infants and children battling high-risk neuroblastoma.