Microarray-based Transcriptional and Epigenetic Profiling of Matrix Metalloproteinases, Collagens, and Related Genes in Cancer

Abstract

Epigenetic parameters (DNA methylation, histone modifications, and miRNAs) play a significant role in cancer. To identify the common epigenetic signatures of both the individual matrix metalloproteinases (MMPs) and the additional genes, the function of which is also linked to proteolysis, migration, and tumorigenesis, we performed epigenetic profiling of 486 selected genes in unrelated non-migratory MCF-7 breast carcinoma and highly migratory U251 glioma cells. Genome-wide transcriptional profiling, quantitative reverse transcription-PCR, and microRNA analyses were used to support the results of our epigenetic studies. Transcriptional silencing in both glioma and breast carcinoma cells predominantly involved the repressive histone H3 Lys-27 trimethylation (H3K27me3) mark. In turn, epigenetic stimulation was primarily performed through a gain in the histone H3 Lys-4 dimethylation (H3K4me2) and H3 hyperacetylation and by a global reduction of H3K27me3. Inactive pro-invasive genes in MCF-7 cells but not in U251 cells frequently exhibited a stem cell-like bivalent mark (enrichment in both H3K27me3 and H3K4me2), a characteristic of developmental genes. In contrast with other MMPs, MMP-8 was epigenetically silenced in both cell types, thus providing evidence for the strict epigenetic control of this anti-tumorigenic proteinase in cancer. Epigenetic stimulation of multiple collagen genes observed in cultured glioma cells was then directly confirmed using orthotopic xenografts and tumor specimens. We suggest that the epigenetic mechanisms allow gliomas to deposit an invasion-promoting collagen-enriched matrix and then to use this matrix to accomplish their rapid migration through the brain tissue.Cell locomotion is a well orchestrated, multi-component, molecular and cellular process that involves multiple and complex regulatory pathways. Proteolysis and proteinases including MMPs, 2 a family of 24 individual enzymes in humans, play an important role in cell function and especially in the processes of cell migration and invasion (1-3). In addition to MMPs, multiple genes and respective cellular proteins, including extracellular matrix (ECM) proteins, integrins, and other adhesion signaling receptors, are also directly involved in cell locomotion. Gene products involved in cell locomotion, angiogenesis, tumor progression, and survival are all potential targets of epigenetic regulation via DNA methylation and histone modifications (4) and by micro-RNA (miRNA) mechanisms (5, 6). In malignancies, DNA methylation is frequently dysregulated. By interfering with the transcription initiation, methylation of the CpG islands (CpGi) inhibits transcription and represses tumor suppressor genes. Acetylation of the core histones H3, H4, H2A, and H2B is normally associated with the activation of gene transcription (7). Acetyl groups are added by a family of histone acetyltransferases and are removed by histone deacetylases. In turn, methylation of the lysine residues in the histone tails may lead to either transcriptional activation or ...

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