Profiling DNA Damage in 3D Histology Samples

Abstract

The morphology of individual cells can reveal much about the underlying states and mechanisms in biology. In tumor environments, the interplay among different cell morphologies in local neighborhoods can further improve this characterization. In this paper, we present an approach based on representation learning to capture similarities and subtle differences in cells positive for γ H2AX, a common marker for DNA damage. We demonstrate that texture representations using GLCM and VAE-GAN enable profiling of cells in both singular and local neighborhood contexts. Additionally, we investigate a possible quantification of immune and DNA damage response interplay by enumerating CD8+ and γ H2AX+ on different scales. Using our profiling approach, regions in treated tissues can be differentiated from control tissue regions, demonstrating its potential in aiding quantitative measurements of DNA damage and repair in tumor contexts.