A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability
- 1Shiv Nadar University
Abstract
Centromeric heterochromatin is maintained by a self-reinforcing loop between DNA methylation (5mC) and histone H3 lysine 9 trimethylation (H3K9me3), yet whether this coupling is preserved at the level of individual chromosomes in cancer has been inaccessible to conventional epigenomic assays, which average signals across cell populations and cannot resolve single-chromosome heterogeneity. Here, we use antibody-functionalized atomic force spectroscopy to simultaneously map 5mC and H3K9me3 at the centromeres of individual metaphase chromosomes from non-tumorigenic, luminal, and triple-negative breast cancer (TNBC) cell models. Co-localized 5mC/H3K9me3 sites are mechanically stiffer than sites carrying either mark alone across the panel, revealing a cooperative biophysical signature of epigenetic crosstalk. Luminal chromosomes acquire the highest mark density, co-localization, and stiffness, whereas TNBC chromosomes show reduced density and diminished, though not absent, co-localization and stiffness, converging toward the low baseline of non-tumorigenic epithelium. TGF-{beta}1-induced epithelial-mesenchymal transition reproduces this attenuated phenotype in luminal cells, linking it directly to a process central to TNBC aggressiveness. These biophysical parameters classify cancer versus non-tumorigenic chromosomes with near-perfect, cross-validated accuracy, and further resolve the two TNBC subtypes using colocalization-derived features alone (macro-F1 = 0.933). These results establish the mechanical consequence of epigenetic mark co-localization as a single-chromosome-resolvable signature of centromeric organization, attenuated in aggressive breast cancer, and demonstrate a force-spectroscopy platform for mechano-epigenetic profiling of cancer chromosomes.
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BibTeX
@misc{agrawal2026nanomechanical,
title = {{A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability}},
author = {T. Agrawal and S. Chakraborty and S. Khanna and S. Sahoo and M. K. Jolly and S. A. Kumar and D. PAUL and S. Majumder and S. Mukherjee and T. Rakshit},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.01.756136},
url = {https://www.biorxiv.org/content/10.64898/2026.10.01.756136v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability
AU - T. Agrawal
AU - S. Chakraborty
AU - S. Khanna
AU - S. Sahoo
AU - M. K. Jolly
AU - S. A. Kumar
AU - D. PAUL
AU - S. Majumder
AU - S. Mukherjee
AU - T. Rakshit
PY - 2026
DA - 2026/10/01
PB - bioRxiv
DO - 10.64898/2026.10.01.756136
UR - https://www.biorxiv.org/content/10.64898/2026.10.01.756136v1
AB - Centromeric heterochromatin is maintained by a self-reinforcing loop between DNA methylation (5mC) and histone H3 lysine 9 trimethylation (H3K9me3), yet whether this coupling is preserved at the level of individual chromosomes in cancer has been inaccessible to conventional epigenomic assays, which average signals across cell populations and cannot resolve single-chromosome heterogeneity. Here, we use antibody-functionalized atomic force spectroscopy to simultaneously map 5mC and H3K9me3 at the centromeres of individual metaphase chromosomes from non-tumorigenic, luminal, and triple-negative breast cancer (TNBC) cell models. Co-localized 5mC/H3K9me3 sites are mechanically stiffer than sites carrying either mark alone across the panel, revealing a cooperative biophysical signature of epigenetic crosstalk. Luminal chromosomes acquire the highest mark density, co-localization, and stiffness, whereas TNBC chromosomes show reduced density and diminished, though not absent, co-localization and stiffness, converging toward the low baseline of non-tumorigenic epithelium. TGF-{beta}1-induced epithelial-mesenchymal transition reproduces this attenuated phenotype in luminal cells, linking it directly to a process central to TNBC aggressiveness. These biophysical parameters classify cancer versus non-tumorigenic chromosomes with near-perfect, cross-validated accuracy, and further resolve the two TNBC subtypes using colocalization-derived features alone (macro-F1 = 0.933). These results establish the mechanical consequence of epigenetic mark co-localization as a single-chromosome-resolvable signature of centromeric organization, attenuated in aggressive breast cancer, and demonstrate a force-spectroscopy platform for mechano-epigenetic profiling of cancer chromosomes.
ER -