Project description:Purpose: Investigate cellular heterogeneity in a fresh human ovarian cancer tissue sample Methods: Enzymatic digestion of fresh tissue sample collected from the operating room to produce single cell suspension. Cells were labelled with fluorescent antibodies to CD3, CD14, CD19, CD20, CD56 and FACS sorted to remove immune cells. The negative population was used for sequencing. Single cells were processed using the Fluidigm C1 Chip to generate barcoded cDNA for each cell. Amplifed cDNA was sequenced using an Illumina HiSeq 2500 machine. Results: Single cell RNA sequence data was obtained for 92 cells and a "bulk" sample of 1000 cells. 26 cells were removed from analysis due to quality control standards. The remaining 66 cells and the bulk sample were analyzed. Conclusion: Single cell RNA sequence analysis reveals heterogeneity in gene expression in cells harvested from a high grade ovarian serous cancer
Project description:We characterized transcriptional patterns of chemotherapy resistance in high-grade serous ovarian cancer (HGSOC) using patient-derived prospective tissue sample pairs before and after treatment at single-cell resolution. Our cohort consists of scRNA-seq data from treatment-naïve and post-neoadjuvant chemotherapy (post-NACT) pairs from 11 homogeneously treated HGSOC patients. After quality control, we obtained 51,786 cells, including 8,806 malignant epithelial (tumor), 8,045 stromal and 34,935 immune cells. Our unbiased analysis reveals how chemotherapy modulates cancer cell states by both subclonal selection and microenvironment boosted transcriptional induction across the homogeneously treated sample cohort. Our results define a cell state that allows biomarker-based prediction and targeting of chemoresistance.
Project description:To understand the recurrence of ovarian cancer, we profiled 13369 single cells from 8 ovarian cancer samples, including 4 primary tumors, 2 peritoneal metastasis and 2 relapse tumors by single cell RNA-seq.
Project description:A collection of 100 ovarian cancer sample gene expression data from Singapore. Frozen archival epithelial ovarian cancer tumors samples from Department of Obstetrics & Gynecology, National University of Singapore dated from 2006 to 2014 were collected and subjected to microarray analysis.
Project description:Integration of several ovarian cancer datasets to identify a reproducible predictors of survival Four microarray datasets from different institutions were reprocessed in a uniform manner, into a single training dataset. Survival analysis was performed and a validation cohort (61 patients from 3 institutions) was profiled using a custom array to confirm the prognostic value of the predictors. The four datasets were obtained from the following reports: Spentzos D, Levine DA, Ramoni MF, et al. Gene expression signature with independent prognostic significance in epithelial ovarian cancer. J Clin Oncol 2004;22:4700-10 Bild AH, Yao G, Chang JT, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature 2006;439:353-7 Marquez RT, Baggerly KA, Patterson AP, et al. Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. Clin Cancer Res 2005;11:6116-26 Zhang L, Volinia S, Bonome T, et al. Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proc Natl Acad Sci U S A 2008;105:7004-9 61 samples