Abstract 657: Aberrant DNA methylation of RUNDC3B in lymphoid malignancies.
Authors: Burmeister Dane W. , Taylor Kristen H. 
Published: August 2014

Pathological research of epigenetic regulation provides a unique insight into disease formation. Heritable changes to DNA conformation can have significant impacts on gene expression without altering the DNA sequence. The RUN domain containing 3B gene (RUNDC3B) has been shown to be differentially expressed in caner types such as, acute lymphoblastic leukemia. This differential expression has been linked to methylation of the gene. The hypothesized function of RUNDC3B is a Rap-2 binding protein which operates regulates GTPases to create biological switches in signaling pathways, such as the Ras signaling pathway. Therefore, aberrant methylation of RUNDC3B could adversely affect Ras signaling and contribute to cancer formation.

Combined bisulfite restriction analysis and methylation specific PCR were used to determine the methylation status of RUNDC3B. This analysis was completed in cell lines from lymphoid malignancies, myeloid malignancies, various solid tumor cancers, and unaffected cell lines. We evaluated 5 regions spanning a CpG island (CGI) in the proximal promoter region of RUNDC3B. Greater than 70% of the regions analyzed in lymphoid malignancies were found to be methylated, whereas, 13.3% of myeloid malignancies, 34.3% of solid tumors, and 10.0% of healthy lymphocyte regions were found to be methylated. This suggests that RUNDC3B may be a useful biomarker for diagnosis and/or prognosis in lymphoid malignancies. Furthermore, this aberrant epigenetic modification may be a significant contributor to pathogenesis of lymphoid malignancies.

To determine the effect of aberrant DNA methylation on RUNDC3B expression, real-time PCR was utilized. Consistent with the methylation data, the lymphoid malignancies were found to be expressed at significantly lower levels than other unmethylated samples. In addition, the methylation of Region 5 of the CGI related strongly with RUNDC3B repression, suggesting a specific set of CpG dinucleotides may be responsible for RUNDC3B silencing.

The function of RUNDC3B is hypothesized based on the presence of a RUN domain. Sequence analysis of RUNDC3B was performed to expand on the hypothesized physiological role. Establishing conserved portions of the promoter region of RUNDC3B supported the conclusion that regulation of this gene is not evolutionarily novel. Analysis across a diverse set of species revealed conservation in transcription factor binding sites, CG content, and RUNDC3B-Rap2 interaction domains.

The data from our experiments has built upon the knowledge of epigenetic regulation of RUNDC3B in cancer. The aberrant methylation leading to RUNDC3B repression is more prevalent in lymphoid malignancies than in several other types of cancer. This provides a clinical role of the gene as a biomarker. As the RUNDC3B gene codes for a regulatory element of the Ras pathway, aberrant epigenetic repression may contribute to the pathogenesis of lymphoid malignancies.

Citation Format: Dane W. Burmeister, Kristen H. Taylor. Aberrant DNA methylation of RUNDC3B in lymphoid malignancies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 657. doi:10.1158/1538-7445.AM2013-657