# Nucleosome Clustering as a Biomarker and Mechanistic Switch for Reprogramming Cells

## TL;DR

This study shows that nucleosome clustering can be altered by biophysical and chemical treatments, leading to tumor-suppressing cell reprogramming in osteosarcoma.

## Contribution

Nucleosome clustering is identified as a novel biomarker and mechanistic switch for cell reprogramming in tumor suppression.

## Key findings

- Biophysical stimuli like vibration and electrical stimulation scatter nucleosome clusters in osteosarcoma cells.
- Pharmacological agents such as Trichostatin A and chaetocin induce nucleosome scattering and tumor-suppressive cell conversion.
- iTS cells show increased KDM3A and KDM4 expression and reduced H3K9me3 levels, indicating epigenetic reprogramming.

## Abstract

Chromatin architecture is highly dynamic, undergoing nanoscale rearrangements throughout the cell cycle and in response to environmental cues. In this study, we employed high-resolution stochastic optical reconstruction microscopy (STORM) to visualize chromatin organization and cellular plasticity at the nanoscale in two osteosarcoma cell lines, U2OS and MG63. To promote a tumor-suppressive bone microenvironment, we applied three biophysical modalities, namely mechanical vibration, electrical stimulation, and optical pulses, each previously linked to altered tumor behavior by reprogramming cells and generating induced tumor-suppressing (iTS) cells. These stimuli enlarged nuclear size and disrupted nuclear envelope integrity, as revealed by increased surface roughness. Critically, all three modalities transiently scattered nucleosome clusters, indicating chromatin decondensation as a hallmark of iTS cell generation. iTS cells exhibited elevated expression of histone demethylases lysine demethylase 3A (KDM3A) and lysine demethylase 4 (KDM4), accompanied by reduced levels of trimethylated histone H3 lysine 9 (H3K9me3). Consistently, pharmacological agents—Trichostatin A as a histone deacetylase inhibitor and chaetocin as a histone methyltransferase inhibitor—induced nucleosome scattering and converted U2OS cells into iTS cells, whose conditioned media exerted tumor-suppressive effects. Our findings highlight nucleosome clustering as a key epigenetic feature responsive to both biophysical and chemical cues, underscoring its role in microscale chromatin remodeling and reprogramming of the tumor microenvironment.