Valproic acid-induced changes of 4D nuclear morphology in astrocyte cells.

Alexandr A Kalinin,Matthew J O’Meara,Ivo D Dinov,Gerald A Higgins,Xiang Wan,Gordon-Victor Fon,Brian D Athey,Xinhai Hou,Jonathan Z Sexton,Alex S Ade,Walter Meixner,Jennifer Lippincott-Schwartz

doi:10.1091/mbc.e20-08-0502

Abstract

Histone deacetylase inhibitors, such as valproic acid (VPA), have important clinical therapeutic and cellular reprogramming applications. They induce chromatin reorganization that is associated with altered cellular morphology. However, there is a lack of comprehensive characterization of VPA-induced changes of nuclear size and shape. Here, we quantify 3D nuclear morphology of primary human astrocyte cells treated with VPA over time (hence, 4D). We compared volumetric and surface-based representations and identified seven features that jointly discriminate between normal and treated cells with 85% accuracy on day 7. From day 3, treated nuclei were more elongated and flattened and then continued to morphologically diverge from controls over time, becoming larger and more irregular. On day 7, most of the size and shape descriptors demonstrated significant differences between treated and untreated cells, including a 24% increase in volume and 6% reduction in extent (shape regularity) for treated nuclei. Overall, we show that 4D morphometry can capture how chromatin reorganization modulates the size and shape of the nucleus over time. These nuclear structural alterations may serve as a biomarker for histone (de-)acetylation events and provide insights into mechanisms of astrocytes-to-neurons reprogramming.

Highlights

Multicellular organisms regulate their cell type and state by selectively exposing portions of their genome for transcription through the spatial and temporal organization of chromatin—dubbed the 4D nucleome (Chen et al, 2015; Cremer et al, 2015; Higgins et al, 2015, 2017a)
We present a detailed characterization of the size and shape of astrocyte nuclei in the context of valproic acid (VPA) treatment
Our findings show that geometric descriptors extracted from voxel and surface-modeled representations of 3D nuclear shapes enabled accurate and interpretable characterization of time-dependent morphological changes in VPA-treated astrocytes

Summary

Introduction

Multicellular organisms regulate their cell type and state by selectively exposing portions of their genome for transcription through the spatial and temporal organization of chromatin—dubbed the 4D nucleome (Chen et al, 2015; Cremer et al, 2015; Higgins et al, 2015, 2017a). Histones accommodate a range of posttranslational modifications, which are controlled by epigenetic proteins that regulate the transcriptional state of the cell and mediate mechanical protection of genome by chromatin rigidity (Yang and Seto, 2007; Stephens et al, 2019). Chemicals that target these proteins can be used to modulate chromatin states and the concomitant cell and nuclear morphology changes observed in human diseases (Marchion et al, 2005; Stephens et al, 2019). VPA shifts the balance toward greater histone acetylation, DNA exposure, and chromatin decondensation; activating transcriptional programs that regulate cellular

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