Similar Datasets
Project description:The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.
2021-04-18 | GSE151569 | GEO
Project description:The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.
2021-04-18 | GSE151430 | GEO
Project description:The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.
2021-04-18 | GSE151357 | GEO
Project description:The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.
2021-04-18 | GSE171833 | GEO
Project description:Multi-functional barcoding enables high resolution study of clonal dynamics
| PRJNA635808 | ENA
Project description:Multi-functional barcoding enables high resolution study of clonal dynamics (scRNA-seq)
| PRJNA636380 | ENA
Project description:Multi-functional barcoding enables high resolution study of clonal dynamics (ATAC-seq)
| PRJNA635809 | ENA
Project description:Multi-functional barcoding enables high resolution study of clonal dynamics (RNA-seq)
| PRJNA635609 | ENA
Project description:Lineage-tracing methods have enabled characterization of clonal dynamics in complex populations, but generally lack the ability to integrate genomic, epigenomic and transcriptomic measurements with live-cell manipulation of specific clones of interest. We developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations. Using ClonMapper, we identified subpopulations of a chronic lymphocytic leukemia cell line with distinct clonal compositions, transcriptional signatures and chemotherapy survivorship trajectories; patterns that were also observed in primary human chronic lymphocytic leukemia. The ability to retrieve specific clones before, during and after treatment enabled direct measurements of clonal diversification and durable subpopulation transcriptional signatures. ClonMapper is a powerful multifunctional approach to dissect the complex clonal dynamics of tumor progression and therapeutic response.
| S-EPMC8691751 | biostudies-literature
Project description:Multi-functional barcoding enables high resolution study of clonal dynamics [multiplexed HG3 ClonMapper recalls]
| PRJNA721170 | ENA