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Variability within rare cell states enables multiple paths towards drug resistance [WM989_DOT1Li]

ABSTRACT: Variability within rare cell states enables multiple paths towards drug resistance [WM989_DOT1Li]

PROVIDER: PRJNA676154 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13036538_1.fastq.gz	Fastqsanger.gz
	SRR13036538_2.fastq.gz	Fastqsanger.gz
	SRR13036539_1.fastq.gz	Fastqsanger.gz
	SRR13036539_2.fastq.gz	Fastqsanger.gz
	SRR13036540_1.fastq.gz	Fastqsanger.gz

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Variability within rare cell states enables multiple paths towards drug resistance.

Project description:Variability within rare cell states enables multiple paths towards drug resistance.

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Variability within rare cell states enables multiple paths towards drug resistance [WM989_WM983b]

Project description:Variability within rare cell states enables multiple paths towards drug resistance [WM989_WM983b]

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Variability within rare cell states enables multiple paths towards drug resistance [WM989_WM983b]

Project description:Molecular differences between individual cells can lead to dramatic differences in cell fate, such as the difference between death versus survival of cancer cells upon treatment with anti-cancer drugs. Despite some progress, these originating differences have largely remained hidden due to the difficulty in determining precisely what variable molecular features lead to which cellular fates. Here, we trace drug-resistant cell fates back to differences in the molecular profiles of their drug-naive melanoma precursors, revealing a rich substructure of variability underlying a number of resistant phenotypes at the single cell level. We make these connections using Rewind, a methodology that combines genetic barcoding with an RNA-based readout to directly capture rare cells that give rise to cellular behaviors of interest. We performed extensive single cell analysis to identify differences in gene expression and MAP-kinase signaling that mark a rare population of drug-naive cells (initial frequency of ~1:1000-1:10,000 cells) that ultimately gives rise to drug resistant clones. We demonstrate that this rare subpopulation has rich substructure and is composed of several distinct subpopulations, and the molecular differences between these subpopulations predict future differences in phenotypic behavior, such as the ultimate proliferative capacity of drug resistant cells. Similarly, we show that treatments that modify the frequency of resistance can allow otherwise non-resistant cells in the drug-naive population to become resistant, and that these new populations are marked by the variable expression of distinct genes. Together, our results reveal the presence of hidden, rare-cell variability that can underlie a range of latent phenotypic outcomes upon drug exposure.

2020-11-12 | GSE161299 | GEO

Variability within rare cell states enables multiple paths towards drug resistance [WM989_DOT1Li]

2020-11-12 | GSE161298 | GEO

Variability within rare cell states enables multiple paths towards drug resistance.

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-11-12 | GSE161300 | GEO

Variability within rare cell states enables multiple paths toward drug resistance.

Project description:Molecular differences between individual cells can lead to dramatic differences in cell fate, such as death versus survival of cancer cells upon drug treatment. These originating differences remain largely hidden due to difficulties in determining precisely what variable molecular features lead to which cellular fates. Thus, we developed Rewind, a methodology that combines genetic barcoding with RNA fluorescence in situ hybridization to directly capture rare cells that give rise to cellular behaviors of interest. Applying Rewind to BRAFV600E melanoma, we trace drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors (initial frequency of ~1:1,000-1:10,000 cells) and relative persistence of MAP kinase signaling soon after drug treatment. Within this rare subpopulation, we uncover a rich substructure in which molecular differences among several distinct subpopulations predict future differences in phenotypic behavior, such as proliferative capacity of distinct resistant clones after drug treatment. Our results reveal hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.

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Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [scRNA-Seq]

Project description:Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [scRNA-Seq]

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Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [ATAC-Seq]

Project description:Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [ATAC-Seq]

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Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [scRNA-Seq]

Project description:Finite replicative potential is a defining feature of non-transformed somatic cells, first established by Leonard Hayflick in vitro using WI-38 human lung fibroblasts. Once proliferative capacity is exhausted due to telomere shortening, cells enter into a state called replicative senescence, which can be avoided through ectopic expression of telomerase reverse transcriptase (hTERT). As WI-38 cells approach replicative arrest, molecular pathways linked to mechanotransduction are induced, including YAP signaling, but the potential interplay between replicative lifespan and the mechanical environment of the cell remains unexplored. Here, we investigate the influence of mechanosensation on the trajectory towards replicative arrest taken by WI-38 cells by growing cells on substrates of varying stiffnesses. Matrix softening slowed proliferation, altered cellular phenotypes, and shortened proliferative lifespan while hTERT expression abrogated or reduced these responses. Our analyses of bulk and single-cell RNA-sequencing and ATAC-sequencing revealed the emergence of a unique G1 transcriptional state on soft substrates, characterized by an AP-1 transcription factor program, which failed to manifest with hTERT expression. Together, these findings reveal how the mechanical environment alters WI-38 cell proliferative lifespan and dictates unique paths towards growth arrest.

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Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [ATAC-Seq]

2024-09-24 | GSE276047 | GEO