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Genomic heterogeneity drives mechanical adaptation in human tumor cells [RNA-seq]

ABSTRACT: Genomic heterogeneity drives mechanical adaptation in human tumor cells [RNA-seq]

PROVIDER: PRJNA1076641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27970200_1.fastq.gz	Fastqsanger.gz
	SRR27970200_2.fastq.gz	Fastqsanger.gz
	SRR27970201_1.fastq.gz	Fastqsanger.gz
	SRR27970201_2.fastq.gz	Fastqsanger.gz
	SRR27970202_1.fastq.gz	Fastqsanger.gz

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Genomic heterogeneity drives mechanical adaptation in human tumor cells [RRBS]

Project description:Genomic heterogeneity drives mechanical adaptation in human tumor cells [RRBS]

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Genomic heterogeneity drives mechanical adaptation in human tumor cells [ATAC-seq]

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Genomic heterogeneity drives mechanical adaptation in human tumor cells [RRBS]

Project description:The progression of many solid tumors is accompanied by temporal and spatial changes in the stiffness of the extracellular matrix (ECM). Cancer cells adapt to soft and stiff ECM through mechanisms that are not fully understood. In particular, it is well known that there is significant genetic heterogeneity from cell to cell in tumors, but how ECM stiffness as a parameter might interact with that genetic variation is not known. Here, we used the method of experimental evolution to study response of genetically variable and clonal tumor cell populations to ECM stiffness. Cell fitness increased on soft ECM over a period of several weeks in genetically variable but not clonal populations. DNA barcode-enabled clonal tracking revealed that sustained culture on soft ECM selects for a few genetic variants. These data provide the first evidence that ECM stiffness exerts natural selection on genetically variable tumor populations. Genome-wide analysis including RNA-seq, ATAC-seq and DNA methylation profiling reveal substantial differences in gene expression between selected populations and ancestral cells which are partially explained by epigenetic modifications. Soft-selected cells are highly migratory with enriched oncogenic signatures and exhibit highly unusual behaviors like spreading and traction force generation on ECMs as soft as 1 kPa. Cell spreading is the directly selected trait but not levels of integrins or adhesion proteins like talin. Overall, these data show that ECM stiffness in solid tumors may drive malignant behaviors through evolution by natural selection.

2026-02-18 | GSE255831 | GEO

Genomic heterogeneity drives mechanical adaptation in human tumor cells [ATAC-seq]

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Genomic heterogeneity drives mechanical adaptation in human tumor cells [RNA-seq]

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PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma

Project description:PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma

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PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma [Human]

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PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma [mouse]

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HIV Nef amplifies mechanical heterogeneity to promote immune evasion

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Cell cycle positioning drives heterogeneity within the pluripotent stem cell compartment

Project description:Heterogeneity in pluripotent cells marks a metastable state where cells may drift between native and lineage-primed populations. While the role for these heterogeneities are unclear, they may reflect the dynamic equilibriums of signaling networks and have a direct effect on differentiation potentialities. Here, we report the role of the cell cycle in establishing heterogeneity of human pluripotent stem cells. By utilizing the FUCCI cell cycle indicator system coupled to fluorescent activated cell sorting (FACS), we have uncovered that the cell cycle drives heterogeneity at the epigenetic, transcriptional and post-transcriptional levels. Our data show widespread dynamics in 5-hydroxymethylcytosine (5hmC) during the cell cycle. Furthermore, transcript profiling by RNA-sequencing identified >500 genes that were cell cycle-regulated, of which the largest cohort of genes were transcriptional regulators. In sum, we demonstrate the role of the cell cycle in coordinating cellular transitions between metastable states in pluripotent stem cells. mRNA sequencing of the cell cycle phases; early & late G1, S and G2/S from human ES cells in triplicate.

2013-12-19 | E-GEOD-53481 | biostudies-arrayexpress

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