Description

Multivariate Image Analysis of Epigenetic Landscape at Single Cell Level Identifies Signature of Glioma Stem Cell Differentiation

Chen Farhy¹, Dmitry Myshkin¹, Santosh Hariharan², David W. Andrews² and Alexey V. Terskikh¹

¹Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; ²Sunnybrook Research Institute, University of Toronto, ON, Canada

Treatment of Glioblastoma multiform (GBM) inevitably results in tumor recurrence due to a highly resistant subpopulation within the GBM mass known as glioma stem cells (GSCs). Failure of cytotoxic drugs to improve clinical outcome led to development of approaches which attempt to induce GSCs differentiation to less tumorigenic cell fates. However, the comprehensive transcriptomic and epigenetic profiling methods required to monitor GCS differentiation are not applicable for the high-throughput screening.

We developed a novel approach, which profiles chromatin organization alterations at single cell level using automated imaging and multiparametric analyses. Microscopic Imaging of Epigenetic Landscape (MIEL) captures the nuclear staining texture obtained by immunofluorescence for histone and DNA modifications to derive textural features. Multivariate analysis and supervised learning models assess the similarity of textures between cell populations and identify classifiers which accurately distinguish them.

Using MIEL we defined the epigenetic signatures of various cell types enabling identification of each cell type with high accuracy. Employing drugs targeting multiple molecular mechanisms as well as treatments known to induce GSC differentiation we categorized the textural alterations associated with specific epigenetics changes to be used in high-throughput screening. Finally, the texture features were used in pseudotemporal ordering algorithms to reveal at single cell level, the dynamics of epigenetic changes during GCS differentiation and identified differences between several GSCs lines.

Our results demonstrate that by providing a snapshot of the entire epigenetic landscape, MIEL allows screening for compounds inducing transient and poorly defined cellular states as well as conducting phenotypic screens.