1. ¹Department of Pathology, UF-Shands Cancer Center Program in Cancer Genetics, Epigenetics, and Tumor Virology, University of Florida College of Medicine, Gainesville, FL, USA
2. ²Department of Biochemistry and Molecular Biology, UF-Shands Cancer Center Program in Cancer Genetics, Epigenetics, and Tumor Virology, University of Florida College of Medicine, Gainesville, FL, USA
3. ³Department of Pathology, Miami Children's Hospital, Miami, FL, USA
4. ⁴National Human Neural Stem Cell Resource, Children's Hospital of Orange County Research Institute, Orange, CA, USA
5. ⁵Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Correspondence: Dr KD Robertson, Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Box 100245, 1600 SW Archer Rd., Gainesville, FL 32610, USA. E-mail: keithr@ufl.edu

Received 31 March 2008; Revised 5 May 2008; Accepted 6 May 2008; Published online 7 July 2008.

Abstract

DNA hypermethylation-mediated gene silencing is a frequent and early contributor to aberrant cell growth and invasion in cancer. Malignant gliomas are the most common primary brain tumors in adults and the second most common tumor in children. Morbidity and mortality are high in glioma patients because tumors are resistant to treatment and are highly invasive into surrounding brain tissue rendering complete surgical resection impossible. Invasiveness is regulated by the interplay between secreted proteases (eg, cathepsins) and their endogenous inhibitors (cystatins). In our previous studies we identified cystatin E/M (CST6) as a frequent target of epigenetic silencing in glioma. Cystatin E/M is a potent inhibitor of cathepsin B, which is frequently overexpressed in glioma. Here, we study the expression of cystatin E/M in normal brain and show that it is highly and moderately expressed in oligodendrocytes and astrocytes, respectively, but not in neurons. Consistent with this, the CST6 promoter is hypomethylated in all normal samples using methylation-specific PCR, bisulfite genomic sequencing, and pyrosequencing. In contrast, 78% of 28 primary brain tumors demonstrated reduced/absent cystatin E/M expression using a tissue microarray and this reduced expression correlated with CST6 promoter hypermethylation. Interestingly, CST6 was expressed in neural stem cells (NSC) and markedly induced upon differentiation, whereas a glioma tumor initiating cell (TIC) line was completely blocked for CST6 expression by promoter methylation. Analysis of primary pediatric brain tumor-derived lines also showed CST6 downregulation and methylation in nearly 100% of 12 cases. Finally, ectopic expression of cystatin E/M in glioma lines reduced cell motility and invasion. These results demonstrate that epigenetic silencing of CST6 is frequent in adult and pediatric brain tumors and occurs in TICs, which are thought to give rise to the tumor. CST6 methylation may therefore represent a novel prognostic marker and therapeutic target specifically altered in TICs.