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Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [RNA-Seq]

ABSTRACT: Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant models of bladder and prostate cancer. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.

ORGANISM(S): Mus musculus

PROVIDER: GSE229780 | GEO | 2023/12/01

REPOSITORIES: GEO

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Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [scDNA-Seq]

Project description:Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant models of bladder and prostate cancer. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.

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Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations

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

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Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease

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2023-09-03 | GSE199261 | GEO

Comparative genomic hybridization by array of Bifodobacterium longum strains exhibiting various human milk oligosaccharide utilization phenotypes and host associations

Project description:Whole genome microarray comparisons (comparative genomic hybridizations) were used to associate genotypic biomarkers among 15 Bifidobacterium longum strains exhibiting various Human Milk Oligosaccharide utilization phenotypes and host associations.

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Tumor stem cells more closely mirror the phenotype and genotype of primary human tumors than do cancer cell lines

Project description:The concept of tumor stem cells (TSCs) provides a new paradigm for understanding tumor biology, although it remains unclear whether TSCs will prove to be a more robust model than traditional cancer cell lines. We demonstrate marked phenotypic and genotypic differences between primary human tumor-derived TSCs and their matched glioma cell lines. TSCs derived directly from primary glioblastomas harbor extensive similarities to normal NSC and recapitulate the genotype, gene expression patterns and in vivo biology of human glioblastomas. By contrast, the matched, traditionally grown tumor cell lines do not secondary to in vitro genomic alterations. These findings suggest that TSCs may be a more reliable model than many commonly utilized cancer cell lines for understanding the biology of primary human tumors. Analysis of gene expression data is described in Lee et al., Cancer Cell, 2006. Keywords: Gene expression profiling of primary GBM tumors and their derivative cells

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Roles of female and male genotype in post-mating responses in Drosophila melanogaster

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