RNA-seq and CUT&Tag-seq datasets for MDA-MB-231 and MCF-10A cells from: Sp1 mechanotransduction regulates breast cancer cell invasion in engineered viscoelastic extracellular matrices

Breast cancer progression involves extensive remodeling of the
extracellular matrix (ECM), including increased stiffness, altered
viscoelasticity (stress relaxation), and elevated collagen levels. While
in vitro experiments have revealed a role for each of these factors in
individually promoting malignant behavior, their combined effects remain
unclear. Here, we engineered alginate-collagen hydrogels with
independently tunable stiffness, stress relaxation, and collagen density
to dissect how the complex ECM environment regulates cancer cell
phenotype. We show that high stiffness, fast stress relaxation, and high
collagen density led to changes in cell morphology, marked by decreased
roundness, and promoted spheroid invasion in both breast cancer and
non-transformed mammary epithelial cells. Single cell migration speed and
displacement were greatest in matrices of high stiffness, low collagen
density, and slow stress relaxation. RNA-seq and Cleavage Under Targets
and Tagmentation (CUT&Tag)-seq revealed that high stiffness and
fast stress relaxing groups were enriched for Sp1 target gene expression
as well as increased Sp1 binding at genomic loci. Notably, analysis of
publicly available claudin-low breast cancer data showed that high
expression of the Sp1-regulated genes in fast stress relaxing groups was
correlated with significantly reduced patient survival. Mechanistically,
we found that phosphorylated Sp1 (T453) exhibited increased nuclear
localization in matrices with high stiffness and fast stress relaxation.
Furthermore, Sp1 phosphorylation was regulated by PI3K and ERK1/2
activity, as well as actomyosin contractility. Our tunable hydrogel
platform reveals that multiple tumor-mimicking cues within complex
viscoelastic microenvironments reinforce malignant traits, with Sp1 acting
as a mechanoresponsive transcription factor that transduces these signals.
RNA-seq dataset for MDA-MB-231 and MCF-10A cells encapsulated for 7 days
in soft or stiff, slow or fast relaxing, and low or high collagen density
alginate-collagen matrices. The RNA-seq dataset has 8 total mechanical
conditions containing 3 replicates per condition for MDA-MB-231 cells and
2 replicates per condition for MCF-10A cells. The dataset contains both
fastq and raw counts (.xlsx) files.  The CUT&Tag-seq
dataset was generated for Sp1 in MDA-MB-231 cells encapsulated
in soft or stiff, slow or fast relaxing, low collagen density
alginate-collagen matrices. The dataset contains has 4 total
mechanical conditions and 2 replicates per condition. This dataset
contains the fastq and bigwig (.bw) files.