DNA hypohydroxymethylation in pediatric central nervous system tumors is associated with CTCF binding sites and reduced survival

Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system tumors. We measured genome-scale 5hmC in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using oxidative and bisulfite treatments. Tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. A linear model tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1 . Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence. These results have implications for emerging molecular neuropathology classification approaches and epigenetic therapeutic strategies in childhood brain tumors. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was supported by a Prouty Pilot Award from the Norris Cotton Cancer Center at Dartmouth-Hitchcock Medical Center. National Institutes of Health R01CA216265, R01GM. Mr. Petersen is supported by the Burroughs-Welcome Fund: Big Data in the Life Sciences at Dartmouth. Ms. Azizgolshani is supported by the S.M. Tenney Fellowship at Dartmouth. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Samples were collected from patients who had provided consent for the use of tissues for research purposes as approved by the committee for the protection of human subjects (Institutional Review Board) at Dartmouth Hitchcock Medical Center. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The pediatric tumor and non-tumor microarray data (IDAT files) were deposited at the Gene Expression Omnibus (GEO) under GSE152561 (http://www.ncbi.nlm.nih.gov/geo/). Data will be made available at publication.