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Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]

ABSTRACT: Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]

PROVIDER: PRJNA471582 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10018149_1.fastq.gz	Fastqsanger.gz
	SRR10018149_2.fastq.gz	Fastqsanger.gz
	SRR10018150_1.fastq.gz	Fastqsanger.gz
	SRR10018150_2.fastq.gz	Fastqsanger.gz
	SRR10018151_1.fastq.gz	Fastqsanger.gz

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Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]

Project description:10X Genomics single cell RNAseq of MCF7 cells treated with bortezomib. Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Importantly, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single cell-derived clones showed that ongoing instability quickly translates into cell line heterogeneity. Testing of the 27 MCF7 strains against 321 anti-cancer compounds uncovered strikingly disparate drug response: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origin and consequence of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

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Genetic and transcriptional variation alters cancer cell line drug response [MCF7]

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Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain L]

Project description:Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain L]

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Genetic and transcriptional variation alters cancer cell line drug response [MCF7]

Project description:10X Genomics single cell RNAseq of MCF7 cells Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Importantly, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single cell-derived clones showed that ongoing instability quickly translates into cell line heterogeneity. Testing of the 27 MCF7 strains against 321 anti-cancer compounds uncovered strikingly disparate drug response: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origin and consequence of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

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Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain L]

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Genetic and transcriptional variation alters cancer cell line drug response

Project description:Genetic and transcriptional variation alters cancer cell line drug response

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Global variation of copy number in the MCF7 genome

Project description:Identify copy number variation in the MCF7 genome Keywords: Copy number variation detection

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Project description:aa

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Macrophages Solvent, AA, LPS, AA+LPS