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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE112856 | GEO | 2019/10/14

REPOSITORIES: GEO

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [micro-environment]

Project description:Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary or metastatic tumors into the blood circulation. Thus, CTCs provide a unique patient biopsy resource to decipher the cellular subpopulations that initiate metastasis and their molecular properties. However, one crucial question is whether CTCs derived from patients recapitulate human metastatic disease in an animal model. Here, we show that CTC lines established from breast cancer patients are capable of generating metastases in mice with a pattern recapitulating most major organs from corresponding patients. To investigate the tumor microenvironment changes in different metastases, we used RNA-seq to analyze expression changes in stromal cells after tumor formation in the brain, lung and bone microenvironments relative to control stromal cells from tumor free mice.

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq]

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]

Project description:Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary or metastatic tumors into the blood circulation. Thus, CTCs provide a unique patient biopsy resource to decipher the cellular subpopulations that initiate metastasis and their molecular properties. However, one crucial question is whether CTCs derived from patients recapitulate human metastatic disease in an animal model. Here, we show that CTC lines established from breast cancer patients are capable of generating metastases in mice with a pattern recapitulating most major organs from corresponding patients. Genome-wide sequencing analyses of metastatic variants identified novel organ tropism-associated markers identified from CTCs and facilitate the development of potential therapies targeting metastatis initiating cells in circulation.

2019-10-14 | GSE112855 | GEO

Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants

Project description:Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [micro-environment]

Project description:Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [micro-environment]

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq]

Project description:Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq]

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Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]

Project description:Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [RNA-seq]

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Targeted Next-Generation Sequencing of Circulating Tumor DNA Mutations among Metastatic Breast Cancer Patients.

Project description:Liquid biopsy through the detection of circulating tumor DNA (ctDNA) has potential advantages in cancer monitoring and prediction. However, most previous studies in this area were performed with a few hotspot genes, single time point detection, or insufficient sequencing depth. In this study, we performed targeted next-generation sequencing (NGS) with a customized panel in metastatic breast cancer (MBC) patients. Fifty-four plasma samples were taken before chemotherapy and after the third course of treatment for detection and analysis. Paired lymphocytes were also included to eliminate clonal hematopoiesis (CH)-related alternatives. A total of 1182 nonsynonymous mutations in 419 genes were identified. More ctDNA mutations were detected in patients with tumors > 3 cm (p = 0.035) and HER2(-) patients (p = 0.029). For a single gene, the distribution of ctDNA mutations was also correlated with clinical characteristics. Multivariate regression analysis revealed that HER2 status was significantly associated with mutation burden (OR 0.02, 95% CI 0-0.62, p = 0.025). The profiles of ctDNA mutations exhibited marked discrepancies between two time points, and baseline ctDNA was more sensitive and specific than that after chemotherapy. Finally, elevated ctDNA mutation level was positively correlated with poor survival (p < 0.001). Mutations in ctDNA could serve as a potential biomarker for the evaluation, prediction, and clinical management guidance of MBC patients with chemotherapy.

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A novel approach for next-generation sequencing of circulating tumor cells.

Project description:BackgroundNext-generation sequencing (NGS) of surgically resected solid tumor samples has become integral to personalized medicine approaches for cancer treatment and monitoring. Liquid biopsies, or the enrichment and characterization of circulating tumor cells (CTCs) from blood, can provide noninvasive detection of evolving tumor mutations to improve cancer patient care. However, the application of solid tumor NGS approaches to circulating tumor samples has been hampered by the low-input DNA available from rare CTCs. Moreover, whole genome amplification (WGA) approaches used to generate sufficient input DNA are often incompatible with blood collection tube preservatives used to facilitate clinical sample batching.MethodsTo address this, we have developed a novel approach combining tumor cell isolation from preserved blood with Repli-G WGA and Illumina TruSeq Amplicon Cancer Panel-based NGS. We purified cell pools ranging from 10 to 1000 cells from three different cell lines, and quantitatively demonstrate comparable quality of DNA extracted from preserved versus unpreserved samples.ResultsPreservation and WGA were compatible with the generation of high-quality libraries. Known point mutations and gene amplification were detected for libraries that had been prepared from amplified DNA from preserved blood.ConclusionThese spiking experiments provide proof of concept of a clinically applicable workflow for real-time monitoring of patient tumor using noninvasive liquid biopsies.

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