Constricted migration is associated with stable 3D genome structure differences in cancer cells

Abstract

To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation, and DNA repair, here, we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi‐C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA‐MB‐231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.

Confined migration induces heterochromatin formation and alters chromatin accessibility

“…Surprisingly, increasing collagen concentrations in 2D culture did not affect heterochromatin levels ( Figure S6 C). Overall, these results suggest that when cells migrate through confined environments in 3D collagen matrices under MMPi, global heterochromatin levels do not show an increase, similar to previous reports ( Golloshi et al, 2022 ; Wang et al., 2018 ). At the same time, these findings point to the difficulty in interpreting results from 3D collagen matrices due to the pleiotropic effects of varying collagen concentrations.…”

“…Although time-lapse microscopy revealed formation of persistent GFP-HP1α enrichments in cells during and after nuclear transit through tight constrictions, indicating an active heterochromatin formation process, and the vast majority of cells that had passed through the constrictions had higher normalized H3K27me3 levels than observed in cells in the “before” population ( Figure 1 G), we cannot rule out the possibility that the observed increase in heterochromatin is a combination of both active induction and passive selection, as suggested by Golloshi et al. regarding the chromatin changes resulted from repeated transwell migration ( Golloshi et al, 2022 ). Taken together, these findings indicate that CMiH is distinct from heterochromatin associated with general migration initiation, which occurs before the onset of migration in 2D and 3D environments ( Gerlitz and Bustin, 2010 ; Segal et al., 2018 ).…”

“…Despite the lack of overt differences in global heterochromatin levels, we reasoned that cells subjected to confined migration may still exhibit local chromatin changes undetected by whole-cell staining levels, as reported by Golloshi et al, 2022. To test this hypothesis, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis, which measures the accessibility of the chromatin genome-wide by transposase-based tagging and fragmentation of the genome (Corces et al, 2017). Experiments were performed in the presence of MMPi treatment to ensure confined pore sizes in the matrices.…”

“…The nuclear deformation and physical stress associated with confined migration can result in nuclear envelope rupture and cause DNA damage ( Denais et al., 2016 ; Irianto et al., 2016 ; Raab et al., 2016 ; Shah et al., 2020 ). Furthermore, recent evidence suggests that migration through confined spaces can lead to rearrangements in 3D genome organization in neutrophils and cancer cells ( Golloshi et al, 2022 ; Jacobson et al., 2018 ), which could affect their transcriptional regulation and cellular functions. However, the effect of confined migration on chromatin modifications and their functional consequences have not been explored.…”

Phenotype Switching of Breast Cancer Cells upon Matrix Interface Crossing

“…It can be assumed that the leading edge of the cell in open matrix creates a high forward stress on the cell, leading to strong deformation of the consecutively following nucleus inducing DNA damage. It is also suggested that such high nuclear stress states might induce epigenetic changes like changes in chromatin methylation and structure leading to the observed alterations in gene expression of the transmigrated cells as discussed also in the cited reports. , This hypothesis is supported by a recent report demonstrating that tumor cells and neutrophil-like cells exhibited changes in genomic variation upon migration through constraining pores, , which in turn enhanced their invasiveness and resistance to anoikis . Dynamic details of such a suggested process deserve further detailed investigations to verify our conclusions.…”