Molecular genetic and epigenetic analysis of NCX2/SLC8A2 at 19q13.3 in human gliomas

M. Qu, H. Jiao, J. Zhao, Z.-P. Ren, A. Smits, J. Kere and M. Nister (2010) Neuropathology and Applied Neurobiology36, 198–210 Molecular genetic and epigenetic analysis of NCX2/SLC8A2 at 19q13.3 in human gliomas Aim: Loss of heterozygosity at 19q13.3 is a common genetic change in human gliomas, indicating yet unknown glial-specific tumour suppressor genes in this chromosome region. NCX2/SLC8A2 located on chromosome 19q13.32 encodes a Na+/Ca2+ exchanger, which contributes to intracellular Ca2+ homeostasis. Its expression is restricted to brain, and it is present neither in other normal tissues nor in gliomas at any significant level. The aim of this study was to investigate if NCX2 might be a tumour suppressor gene involved in glioma. Methods: We performed a systematic analysis of NCX2 in 42 human gliomas using microsatellite analysis for evaluation of loss of heterozygosity at 19q, DNA sequencing and DNA methylation analysis. Results: Except for three known intragenic single nucleotide polymorphisms, rs12459087, rs7259674 and rs8104926, no NCX2 sequence variations were detected in any of the tumour samples. Furthermore, a CpG island in the 5′ promoter region of NCX2 was unmethylated. Interestingly, the CpG sites of three gene-body CpG islands located in exon 2, intron 2–3 and exon 3 and of a 5′ CpG-rich area relevant to so-called CpG island shore of NCX2 were methylated in all eight glioma samples and in three established glioma cell lines tested. Surprisingly, NCX2 could be activated by addition of the DNA methylation inhibitor 5-aza-2′-deoxycytidine to glioma cell lines in which NCX2 was completely silent. Conclusion: Results indicate that DNA methylation may play a key role in the transcriptional silencing of NCX2.