125P - Detection and analysis of medulloblastoma subtype-specific copy number variations from RNA-seq data for improved risk-based subtype classification

Background

Medulloblastoma (MB) is an aggressive brain tumor that comprises 30% of malignant central nervous system cancers in childhood. A multi-omic approach has classified MB into four molecular groups: WNT, SHH, Group 3 (Gr3) and Group 4 (Gr4). However, this classification overlooks existing heterogeneity, as recent research has identified additional subtypes with varying prognoses. Given recent studies linking copy-number variations (CNVs) to prognosis, this research aimed to evaluate the potential of RNA-sequencing in detecting subtype-specific CNVs and improving risk-based stratification.

Methods

The study included 108 pediatric MB patients from five publicly available cohorts in Gene Expression Omnibus (GSE143940, GSE151519, GSE158413, GSE181293 & GSE243795) and an in-house cohort of 54 patients sequenced using Illumina technology (NovaSeq 6000 System, ≈150M 100bp PE reads). STAR v2.7.10a was used for the alignment and featureCounts for quantification, with Ensembl 108 reference genome (hg38). Variant calling was performed following the Genome Analysis Toolkit (v4.5.0.0) workflow. Finally, superFreq and RNAseqCNV were used for digital karyotyping.

Results

The analysis of CNVs showed 632 events in RNAseqCNV and 656 in superFreq, with a 93% overlap. Monosomy 6, hallmark of WNT MBs, was detected in 80.6% of cases. In SHH, losses of chr9q and 10q were found in 41% and 26% of patients respectively. Gains in chr2, 3q and 9p, and losses in chr14q and 17p, linked with diverse prognosis SHH-α, β or Δ subtypes, were observed. In Gr3, 68% of patients showed an event in chr17, i17q being the most recurrent alteration. Also, 45% and 39% of patients showed alterations in chr7 and 8 respectively, linked to Gr3-II/III (poor prognosis) or Gr3-IV (good prognosis) subtypes. Gr3-III specific losses of chr10q and 16q were detected. Lastly, 81% of Gr4 MBs showed i17q or chr17q gain, hallmark of Gr4 MBs. Favorable-risk gains in chr7 and losses in chr8 and 11 appeared in 47%, 30% and 22% of patients respectively, common traits of Gr4-VI/VII subtypes.

Conclusions

These results suggest that RNA-sequencing could be an effective tool for detecting subtype-specific CNVs and facilitating risk-based stratification in MB.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

University of the Basque Country (UPV/EHU).

Funding

Basque Foundation for Health Innovation and Research (IT1559-22), Asociación Pablo Ugarte APU (BC/A/14/015), Pequerropa (BC/A/15/010), the projects from EITB Media (BIO20/CI/013BCB and BIO20/CI/15BCB) and the Department of Education of the Basque Government (PRE_2023_1_0035).

Disclosure

All authors have declared no conflicts of interest.