Abstract
Purpose: 5-Hydroxymethylcytosine (5-hmC) is an epigenetic marker of open chromatin and active gene expression. We profiled 5-hmC with Nano-hmC-Seal technology using 10 ng of plasma-derived cell-free DNA (cfDNA) in blood samples from patients with neuroblastoma to determine its utility as a biomarker. Experimental Design: For the Discovery cohort, 100 5-hmC profiles were generated from 34 well children and 32 patients (27 high-risk, 2 intermediate-risk, and 3 low-risk) at various time points during the course of their disease. An independent Validation cohort encompassed 5-hmC cfDNA profiles (n ¼ 29) generated from 21 patients (20 high-risk and 1 intermediate-risk). Metastatic burden was classified as high, moderate, low, or none per Curie metaiodobenzylguanidine scores and percentage of tumor cells in bone marrow. Genes with differential 5-hmC levels between samples according to metastatic burden were identified using DESeq2. Results: Hierarchical clustering using 5-hmC levels of 347 genes identified from the Discovery cohort defined four clusters of samples that were confirmed in the Validation cohort and corresponded to high, high-moderate, moderate, and low/no metastatic burden. Samples from patients with increased metastatic burden had increased 5-hmC deposition on genes in neuronal stem cell maintenance and epigenetic regulatory pathways. Further, 5-hmC cfDNA profiles generated with 1,242 neuronal pathway genes were associated with subsequent relapse in the cluster of patients with predominantly low or no metastatic burden (sensitivity 65%, specificity 75.6%). Conclusions: cfDNA 5-hmC profiles in children with neuroblastoma correlate with metastatic burden and warrants development as a biomarker of treatment response and outcome.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1309-1317 |
| Number of pages | 9 |
| Journal | Clinical Cancer Research |
| Volume | 26 |
| Issue number | 6 |
| DOIs | |
| State | Published - Mar 15 2020 |
Funding
This work was supported in part by the Alex's Lemonade Stand Foundation (to S.L. Cohn); a kind gift from Barry & Kimberly Fields (to S.L. Cohn and C. He); Neuroblastoma Children's Cancer Society (to S.L. Cohn); the Children's Neuroblastoma Cancer Foundation (to S.L. Cohn); the Matthew Bittker Foundation (to S.L. Cohn); the Super Jake Foundation (to S.L. Cohn); and the Elise Anderson Neuroblastoma Research Fund (to S.L. Cohn). Also supported by the NIH K08CA226237 (to M.A. Applebaum) and the Ludwig Center at the University of Chicago (to C. He). C. He is a Howard Hughes Medical Institute Investigator. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. The authors thank the Center for Research Informatics of the University of Chicago for use of the Gardner High-Performance Computing cluster and the Cancer Center Support Grant (P30 CA014599) for support of the Genomics Core Facility.
ASJC Scopus subject areas
- General Medicine
