Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of isolated tumor cells from high grade serous ovarian cancer (HGSOC) patients

ABSTRACT: Tumor cells were isolated from solid tumors or ascites from HGSOC patients and enriched for EpCAM expression by antibody magnetic beads (affinity)-based methods and large RNAs (> 200 nt) sequenced (50 bp paired ends) after rRNA depletion (RiboZero). Expression differences between patients with miliary and non-miliary peritoneal tumor spreading were used for a search for new targeted therapies and for biological annotion.

INSTRUMENT(S): QIAcube (Qiagen), epMotion 5075 automated pipetting system (Eppendorf, Hamburg, Germany), Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Dietmar Pils

PROVIDER: E-MTAB-7674 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Peritoneal tumor spread in serous ovarian cancer-epithelial mesenchymal status and outcome.

Auer Katharina K Bachmayr-Heyda Anna A Aust Stefanie S Sukhbaatar Nyamdelger N Reiner Agnes Teresa AT Grimm Christoph C Horvat Reinhard R Zeillinger Robert R Pils Dietmar D

Oncotarget 20150701 19

<h4>Unlabelled</h4>In this study we aimed to analyze the biological mechanisms underlying apparently different modes of peritoneal tumor spread in serous ovarian cancer: miliary (widespread, millet-like lesions) versus non-miliary (bigger, exophytically growing implants). Tumor tissues and ascites from 23 chemotherapy naive patients were analyzed by RNA-sequencing and flow cytometry. On the basis of differential gene expression between miliary and non-miliary, gene signatures were developed. A c ...[more]

PMID: 25991672

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Project description:Clear cell renal cell carcinoma (ccRCC) initiated from the renal epithelium is the most prevalent histological type of adult kidney cancers. Dissecting intratumoral heterogeneity (ITH) of ccRCC has leveraged to extend our knowledge on how primary tumors harboring driver mutations evolve and spread to other sites. The cellular fractions within and across the primary (pRCC) and metastatic RCC (mRCC) are heterogeneous in both their genetic and biological features determining the variability in clinical aggressiveness and sensitivity to the therapy. To achieve sustainable therapeutic benefit with targeted agents in mRCC, the effective target should focus on signaling pathways that are related to driver mutations occurred early in the clonal evolution of the disease and thus should be common to primary tumor and metastatic sites. Considering that extensive genetic heterogeneity may result in drug response variability among patients and treatment resistance, the tailored strategies for metastatic RCC is urgently needed. Here, we analyze single-cell RNA-seq (scRNA-seq) data from a matched primary RCC (pRCC) and lung metastasis (mRCC) to dissect ITH at the highest resolution to date with the objective of discovering the better therapeutic regimen. In order to identify successful clonal propagation from patient to PDX samples and understand pathogenesis from primary to metastatic RCC, we performed whole-exome sequencing (WES, n=4) and matched aCGH (n=4) on bulk tumor samples. And we utilized single-cell RNA sequencing (scRNA-seq) to model and dissect functional heterogeneity acroass primary and metastatic RCC tumors. We checked whether of capturing live one cell, not more cells, in microfluidics by fluorescent microscopic observation. To construct RNA sequencing libraries, we performed further quality controls including adequate quantities and qualities of amplified transcriptomes respectively from single cells. Tumor cells from the parental mRCC (n=34), PDX-mRCC (n=36) and PDX-pRCC (n=46) were finally analyzed in this study after filtering out poor quality cells.

Dataset Information

RNA-seq of isolated tumor cells from high grade serous ovarian cancer (HGSOC) patients

Publications

Peritoneal tumor spread in serous ovarian cancer-epithelial mesenchymal status and outcome.

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