Transcriptomic profiles of ovarian cancer cells isolated from paired cancer ascites before and after chemotherapy
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ABSTRACT:
PROVIDER: PRJNA1010738 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25795481_1.fastq.gz | Fastqsanger.gz | |||
| SRR25795481_2.fastq.gz | Fastqsanger.gz | |||
| SRR25795482_1.fastq.gz | Fastqsanger.gz | |||
| SRR25795482_2.fastq.gz | Fastqsanger.gz | |||
| SRR25795483_1.fastq.gz | Fastqsanger.gz |
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Project description:Ovarian cancer is characterized by transcoelomic metastasis into the peritoneal cavity. The peritoneal malignant ascites is enriched with ovarian cancer cells and a small amount of tumor-associated immune cells which create a unique microenvironment actively contributing to progression of the disease. However, it is remain unclear how cancer cells communicate to its local environment under the influence of chemotherapy. To address this issue, we performed LC-MS/MS analyses of ovarian cancer ascites from the same patients before and after chemotherapy. We found that neoadjuvant chemotherapy causes a significant changes in the composition of ascites, and these changes are similar in samples obtained from all patients (n=10). Functional annotation of upregulated proteins with the use of KEGG and GO databases revealed that malignant ascites after chemotherapy were enriched with the cluster of spliceosomal proteins. These splicing factors were linked to induction of epithelial-to-mesenchymal transition leading to a more aggressive phenotype of cancer cells.
2024-05-29 | PXD019327 | Pride
Project description:Chemotherapy in complex with surgical removal remain the most common approaches in cancer treatment, but their effectiveness is limited by the emergence of chemoresistance. In order to reveal changes in transcriptomic profiles of cancer cells remaining after platinum-based chemotherapy, we created primary cultures of cancer cells isolated from paired ascites of ovarian cancer patients taken at the time of diagnosis and after neoadjuvant chemotherapy. Enrichment analysis revealed significant activation of genes associated with DNA repair and cell cycle regulation in tumor cells after chemotherapy.
2024-04-24 | GSE241908 | GEO
Project description:Ovarian cancer is characterized by transcoelomic metastasis into the peritoneal cavity. The peritoneal malignant ascites is enriched with ovarian cancer cells and a small amount of tumor-associated immune cells which create a unique microenvironment actively contributing to progression of the disease. However, it is remain unclear how chemonaive and post-chemotherapy ovarian cancer ascitic fluids influence on cancer cells. To address this issue, we performed RNAseq analysis of primary cultures of ovarian cancer cells incubated for 3 days in the presence of ascites from the same patients before and after chemotherapy. We found that ascites after therapy causes a significant changes in transcriptomic profiles of cancer cells, and these changes are similar in samples obtained from all patients (n=4). Enrichment analysis of differentially expressed genes in tumor cells incubated with ascites after chemotherapy identified prominent up-regulation of genes associated with DNA repair, mitotic cell cycle regulation, and cell cycle checkpoints. These findings demonstrate how ascitic fluids persisted after chemotherapy can contribute to the emergence of tumor chemoresistance during short time period.
2024-04-24 | GSE241909 | GEO
Project description:Ovarian cancer is characterized by transcoelomic metastasis into the peritoneal cavity. The peritoneal malignant ascites is enriched with ovarian cancer cells and a small amount of tumor-associated immune cells which create a unique microenvironment actively contributing to progression of the disease. However, it remains unclear how cancer cells communicate to its local environment under the influence of chemotherapy. To address this issue, we performed LC-MS/MS analyses of several primary cultures of ovarian cancer cells from chemonaive malignant ascites incubated for 3 days with autologous pre- or post-chemotherapy ascitic fluids. Enrichment analysis identified prominent upregulation of proteins associated with pathways of DNA repair and cell cycle regulation in tumor cells incubated with ascitic fluids after chemotherapy. Consistently with these data, ascites after therapy increased the resistance of ovarian cancer cells to cisplatin. These findings demonstrate that under stress condition cancer cells can secrete signaling molecules into the extracellular space and contribute to the emergence of tumor chemoresistance during short time period.
2024-05-29 | PXD045647 | Pride
Project description:Purpose: Malignant ascites is an abnormal accumulation of fluid within the peritoneal cavity, caused by metastasis of several cancer types including colorectal cancer. Cancer cells in ascites reflect poor prognosis and can be a source of recurrence. They also represent a good source of specimens for the study of tumor heterogeneity. Single-cell RNA-sequencing (scRNA-seq) has recently emerged as a powerful tool for exploring and characterizing cellular heterogeneity in both normal tissues and cancers. However, molecular profiles of malignant ascites cells in response to treatment are still poorly understood. Materials and Methods: We have performed scRNA-seq of ascites-derived cells from a colorectal cancer patient to profile and characterize the cellular heterogeneity and different expression hallmarks within the cell populations before and after a chemotherapy treatment. The effect of different single cell preparation protocols, namely, manual and enzymatic methods, on cell viability and gene expression were also assessed. Results: Unbiased clustering of 19,653 cells in total reveals 12 sub-clusters with unique transcriptomic patterns from four major cell types: epithelial cells, myeloid cells, fibroblast, and lymphocytes. Interestingly, the percentages of cells recovered from different cell types appeared to be influenced by the preparation protocols; enzymatic and mechanical separations, with more than 90% reduction in myeloid cell number when enzymatic method was used. Subcluster analysis of epithelial cell populations before and after chemotherapy treatment identified distinct cell clusters with unique transcriptomic profiles. Moreover, there were only three out of 11 epithelial subclones with more than 50% reduction in tumor cell number after treatment. This finding indicated that most clones were resistant to the treatment, which reflected the poor treatment outcome observed in our patient. Conclusions: Overall, our study underscores cellular heterogeneity within malignant ascites and uncovers the gene expression profile of colorectal cancer ascites-derived cells in single-cell resolution. Our findings emphasize the potential benefit of using scRNA-Seq to monitor real-time treatment response in cancer patients.
2021-12-15 | GSE155953 | GEO
Project description:To characterize the spatial tumor microenvironment (TME) of high-grade serous ovarian cancer (HGSC) at the single cell level, we performed single-cell RNA sequencing (scRNA-seq) on 48 tumor or ascites samples from 29 HGSC patients. This data set includes paired scRNA-seq data from chemo-naive and post-neoadjuvant chemotherapy (IDS) samples of 22 HGSC patients.
2024-10-08 | GSE266577 | GEO
Project description:Peritoneal carcinomatosis with malignant ascites is associated with dismal prognosis in gastric cancer. Malignant ascites is the most relevant body fluid in which to seek diagnostic biomarkers for peritoneal carcinomatosis. We aimed to identify and validate ascites-derived circulating microRNAs (miRNAs) that are differentially expressed between liver cirrhosis-associated benign ascites (LC-ascites) and gastric cancer-associated malignant ascites (GC-ascites). MiRNA expression levels were investigated in three independent cohorts. Overall, 165 ascites samples (73 LC-ascites and 92 GC-ascites) were obtained from the National Biobank of Korea. Initially, microarrays were used to screen the expression levels of 2,006 miRNAs in the discovery cohort (n = 22). Subsequently, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analyses were used to validate the expression levels of selected miRNAs in the training (n = 70) and validation (n= 73) cohorts. In addition, the levels of carcinoembryonic antigen (CEA), a commonly used tumor marker, were determined in the ascites samples. Expression levels of miR-574-3p, miR-181b-5p, miR-4481, and miR-181d were significantly lower in the GC-ascites samples than in the LC-ascites samples, and miR-181b-5p showed the best diagnostic performance for GC-ascites (area under the curve [AUC] = 0.798 and 0.846 for the training and validation cohorts, respectively). The diagnostic performance of CEA for GC-ascites was improved if CEA and miR-181b-5p were analyzed together (AUC = 0.981 and 0.946 for the training and validation cohorts, respectively). Overall, we identified ascites-derived circulating miRNAs capable of differentiating non-malignant ascites and GC-ascites, and demonstrated that the combined use of miR-181b-5p and CEA produces the optimal diagnostic yield.
2019-02-12 | GSE126399 | GEO
Project description:Gastric cancer is one of the most lethal malignancies with high mortality and gastric cancer-specific biomarker is need due to the lack of specific method for early screening, diagnosis, and prognosis of the patients with gastric cancer. Ascites is known for an important source for conducing biomarker discovery because it contains the secreted proteins from malignant cells, growth factors, and cytokines. In this study, we have conducted a comprehensive proteome study using ascites of patients with inflammatory diseases and gastric cancer. In the discovery stage, we have identified 2761 ascites-specific proteins, where 234 proteins were quantitated using the label free quantitation method, the normalized spectral abundance factor (NSAF); 152 and 82 proteins showed up and down-regulated pattern, respectively. Our ascites proteome can be used as baseline data for the discovery of novel biomarkers of the gastric cancer.
2018-04-16 | PXD002213 | Pride
Project description:Cancer recurrence and chemoresistance are the leading causes of death in high-grade serous ovarian cancer (HGSOC) patients. However, the unique role of the immune environment in tumor progression for relapsed chemo-resistant patients remains elusive. In single-cell resolution, we characterized a comprehensive multi-dimensional cellular and immunological atlas from tumor, ascites, and peripheral blood of a chemo-resistant patient at different stages of treatment. Our results highlight a role in recurrence and chemoresistance of the immunosuppressive microenvironment in ascites, including MDSC-like myeloid and hypo-metabolic γδT cells, and of peripheral CD8+ effector T cells with chemotherapy-induced senescent/exhaustive. Importantly, paired TCR/BCR sequencing demonstrated relative conservation of TCR clonal expansion in hyper-expanded CD8+ T cells and extensive BCR clonal expansion without usage bias of V(D)J genes after chemotherapy. Thus, our study suggests strategies for ameliorating chemotherapy-induced immune impairment to improve the clinical outcome of HGSOC.
2022-09-15 | GSE213243 | GEO
Project description:We present evidence for an autocrine cytokine network in human ovarian cancer that has paracrine actions on the tumour microenvironment. In experiments using bioinformatics analysis of large gene expression array datasets and ovarian cancer biopsies, we found that the inflammatory cytokines TNF-α and IL-6, the chemokine receptor CXCR4 and its ligand CXCL12, are co-regulated in malignant cells. We named this co-regulation the TNF network. We had access to a unique set of ascites cell samples from patients with advanced ovarian cancer treated with the therapeutic anti-human TNF-α antibody infliximab. Serial samples pre and during treatment were obtained during paracentesis (drainage of ascites fluid for symptomatic relief). In nine of these patients there was sufficient mRNA available for gene expression profile analysis before treatment. The Affymetrix GeneChip Human Genome U133Plus 2.0 arrays were used to define gene expression profiles in each of the ascites cell samples.
2009-12-31 | E-GEOD-18681 | biostudies-arrayexpress