Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma
Open accessAbstract
BACKGROUND: Epigenetic mechanisms such as DNA methylation and histone modifications are important regulators of gene expression and are frequently involved in silencing tumor suppressor genes. METHODS: In order to identify genes that are epigenetically regulated in neuroblastoma tumors, we treated four neuroblastoma cell lines with the demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-dC) either separately or in conjunction with the histone deacetylase inhibitor trichostatin A (TSA). Expression was analyzed using whole-genome expression arrays to identify genes activated by the treatment. These data were then combined with data from genome-wide DNA methylation arrays to identify candidate genes silenced in neuroblastoma due to DNA methylation. RESULTS: We present eight genes (KRT19, PRKCDBP, SCNN1A, POU2F2, TGFBI, COL1A2, DHRS3 and DUSP23) that are methylated in neuroblastoma, most of them not previously reported as such, some of which also distinguish between biological subsets of neuroblastoma tumors. Differential methylation was observed for the genes SCNN1A (p < 0.001), PRKCDBP (p < 0.001) and KRT19 (p < 0.01). Among these, the mRNA expression of KRT19 and PRKCDBP was significantly lower in patients that have died from the disease compared with patients with no evidence of disease (fold change -8.3, p = 0.01 for KRT19 and fold change -2.4, p = 0.04 for PRKCDBP). CONCLUSIONS: In our study, a low methylation frequency of SCNN1A, PRKCDBP and KRT19 is significantly associated with favorable outcome in neuroblastoma. It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas.
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Basic analysis of β values works well for detecting large DNA methylation differences, such as between tissues or tumor-normal pairs.
“The β values are indeed fairly stable and the basic analysis method works well, particularly for the detection of large differences, for example between tissues or tumor-normal pairs [8].”
From A data-driven approach to preprocessing Illumina 450K methylation array data (2013) · cites this paper as [8]
The Methods define β values, and the Results (Differential methylation analysis; page unavailable) show that comparing them detected differences between neuroblastoma patient groups. The Discussion describes DNA methylation measurement as robust and stable. The paper does not establish that basic β-value analysis works particularly well for large differences between tissues or tumor–normal pairs. (LLM, conf=0.83)
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- Authors
- Carén, H., Djos, A., Nethander, M., Sjöberg, R.-M., Kogner, P., Enström, C., Nilsson, S., & Martinsson, T.
- Affiliations
- Sahlgrenska University Hospital (SE)
- University of Gothenburg (SE)
- Karolinska University Hospital (SE)
- Uppsala University (SE)
- Chalmers University of Technology (SE)
- Corresponding author
- Carén, Helena
- Venue
- BMC Cancer
- Published
- 2011-02-11
- Volume
- 11
- Issue
- 1
- Pages
- 66-66
- ISSN
- 1471-2407 (ISSN-L)
- PMC
- PMC3045360
- OpenAlex
- W2122906783
- Cited by
- 74
- References
- 47
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 4 · 2021: 4 · 2020: 1 · 2019: 5 · 2018: 1 · 2017: 3 · 2016: 4 · 2015: 6 · 2014: 4 · 2013: 13 · 2012: 14
- FWCI
- 7.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Cancer (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Gothenburg University Publications Electronic Archive (Gothenburg University) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Chalmers Publication Library (Chalmers University of Technology) (submittedVersion)
- Chalmers Research (Chalmers University of Technology) (submittedVersion)
- Funders
- Children's Cancer Foundation
- Cancerfonden
- Karolinska Institutet
- Knut och Alice Wallenbergs Stiftelse
- Akademiska Sjukhuset
- Sahlgrenska Universitetssjukhuset
- Uppsala Universitet
- Sahlgrenska Akademin
- Topics
- Health Sciences › Medicine › Neurology › Neuroblastoma Research and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Health Sciences › Medicine › Genetics › Glioma Diagnosis and Treatment
- Keywords
- neuroblastoma, DNA methylation, epigenetic regulation, prognostic factors, patient outcomes, azacitidine, trichostatin A, histone deacetylase inhibition, keratin 19, SCNN1A, tumor suppressor gene silencing, gene expression, childhood cancer, treatment stratification
- MeSH terms
- Algorithms, Brain Neoplasms, Humans, Neuroblastoma, Prognosis, Biomarkers, Tumor, Genes, Tumor Suppressor, DNA Methylation, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Epigenesis, Genetic, Cell Line, Tumor, Microarray Analysis, Genes, Neoplasm, Genetic Association Studies
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