Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis

Non-small cell lung cancer (NSCLC) is one of the most commonly diagnosed and deadliest cancers worldwide, owing in large part to roughly half of all patients initially presenting with both primary and metastatic disease. While the major events in the metastatic cascade have been identified, a mechanistic understanding of how NSCLC routinely, successfully colonizes the brain is largely unknown. Recent studies have begun demonstrating the role of epigenetic mis-regulation within tumorigenesis as well as in the metastatic process, including widespread changes in DNA methylation and histone modifications. To better understand the role of DNA methylation alterations in NSCLC metastasis to brain, we measured DNA methylation during disease progression for 12 patients, globally profiling the methylation of their normal lung, primary lung tumor, and brain metastasis. We found that the variation in methylation is just as great; albeit less coordinated across genomic features, during metastatic spread as compared to primary tumorigenesis. The greatest recurrent methylation changes during metastatic progression occurred over DNA methylation valleys (DMVs) harboring H3K9me3 as well as bivalent marks H3K27me3 and H3K4me1 enrichment in normal lung. Mapping EZH2, the catalytic subunit of polycomb repressive complex 2 (PCR2), binding locations in H1299, a lymph node-derived lung cancer cell line, revealed a loss of EZH2 binding within DMVs accompanied by an increase in DNA methylation, exemplifying epigenetic switching. The vast majority of these differentially methylated region-associated DMVs harbor developmental genes, suggesting that altered epigenetic regulation of developmentally important genes may confer a selective advantage during metastatic progression. Samples: 2 separate ChIP-seq replicates were completed for the identification of EZH2 in the cell line H1299. Both replicates consist of paired-end reads. Data are included from both the EZH2 IP and input.