LA1-5s

Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations

Neuroblastoma (NB) is a pediatric cancer with heterogeneous differentiation stages. Global DNA methylation loss and 5-hydroxymethylcytosine (5hmC) alterations are cancer hallmarks. Narmontė et al. used single-base resolution methods (hmTOP-seq, uTOP-seq) to construct 5hmC maps and identify partially methylated domains (PMDs) in NB cell subpopulations, aiming to uncover lineage-specific epigenetic signatures and their clinical relevance.

They evaluated 5hmC levels in NB cell lines and subpopulations, BE(2)-C (I-type) and BE(2)-M17 (N-type), and LA1-55n (N-type) and LA1-5s (S-type), by HPLC-MS/MS (Fig. 1A, B). All samples showed low global 5hmC (0.0025-0.006%) versus neural tissues. Hypoxia increased 5hmC 2.5-fold without affecting 5mC, confirmed by elevated HIF-1α/2α (Fig. 2). Genome-wide 5hmCG mapping identified 1.67 M genomic CGs (5.9%) with good replicate correlation (r = 0.88), plus ~30,000 5hmCH sites (Fig. 3A, D). h-density normalization improved correlation to 0.95 (Fig. 3B, C). 5hmCG and h-density were enriched in enhancers, introns, 3'UTRs, CGI shores/shelves, and HIF-2 response elements, but depleted in intergenic regions. Non-coding RNAs and transcribed processed pseudogenes showed highest enrichment, linking 5hmC to active transcription.