Effects of Culture Condition on Epigenomic Profiles of Brain Tumor Cells

Personalized cancer medicine offers the promise of more effective treatments that are tailored to an individual’s own dynamic cancer phenotype. Meanwhile, tissue-engineering approaches to modeling tumors may complement these advances by providing powerful new strategies for understanding the adaptation dynamics occurring during treatment. However, in both of these areas, new tools will be required to gain a full picture of the genetic and epigenetic regulators of phenotype dynamics occurring in the small populations of cells that drive resistance. In this study, we perform epigenomic analysis of brain tumor cells that are collected from microengineered three-dimensional tumor models, overcoming the challenges associated with the small numbers of cells contained within these microtissue niches, in this case collecting ∼1000 cells per sample. Specifically, we use a high-resolution epigenomic analysis method known as microfluidic-oscillatory-washing-based chromatin immunoprecipitation with sequencing (MOWChIP-seq) to analyze histone modification patterns (H3K4me3). We identified gene loci that are associated with the H3K4me3 modification, which is generally a mark of active transcription. We compared H3K4me3 profiles in standard 2D cultures and 3D cultures based on type I collagen hydrogels, under both normoxic and hypoxic conditions. We found that culture dimensionality drastically impacted the H3k4me3 profile and resulted in differential modifications in response to hypoxic stress. Differentially H3K4me3-marked regions under the culture conditions used in this study have important implications for gene expression differences that have been previously observed. In total, our work illustrates a direct connection between cell culture or tissue niche condition and genome-wide alterations in histone modifications, providing the first steps toward analyzing the spatiotemporal variations in epigenetic regulation of cancer cell phenotypes. This study, to the best of our knowledge, also represents the first time broad-spectrum epigenomic analysis has been applied to small cell samples collected from engineered microtissues.