Profiling gene expression changes in primary ovarian tumors compared to matched metastasis
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ABSTRACT:
PROVIDER: PRJNA564846 | ENA |
REPOSITORIES: ENA
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Project description:Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer related deaths among women in USA. Most patients have metastatic disease at the time of diagnosis and this causes the poor prognosis. For a comprehensive understanding of the gene expression changes accompanying ovarian cancer metastasis, we isolated RNA from 11 pairs of matched primary tumors and metastasis from OC patients and sequenced them. Library preparation and next generation RNA sequencing was carried out at the Center for Genomics and Bioinformatics core facility, Indiana University, Bloomington. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).
2019-10-18 | GSE137237 | GEO
Project description:Ovarian cancer is the most frequent cause of cancer death in women and the leading cause of death related to gynecological cancer, accounting for 5% of estimated cancer deaths. Due to its asymptomatic nature at early stages, most ovarian cancers were diagnosed at an advanced stage, with distant metastasis in the abdominal cavity. Cancer metastasis is the primary cause of morbidity, and contributes to 95% of cancer-related deaths. Metastatic ovarian cancer is closely related with recurrence and drug resistance, rendering metastasis as the major challenge in the course of ovarian cancer treatment. Thorough understanding of ovarian cancer metastasis is believed to contribute to improve cancer cure rates, while it is still not well elucidated. One important aspect of ovarian cancer metastasis research is the identification of driver molecular. To identify proteins required for ovarian cancer metastasis, we carried out unbiased high-throughput screening by comparing the expression profile of ovarian cancer primary and metastasis tissues.
2023-01-20 | GSE222982 | GEO
Project description:Profiling gene expression changes in primary ovarian tumors compared to matched normal fallopian tubes
| PRJNA564844 | ENA
Project description:Our aim was to decipher the underlying molecular mechanism of synchronous ovarian metastasis of gastric cancer. We hereby conducted transcriptome sequencing of triple-matched samples including normal gastric mucosa, primary gastric cancer and ovarian metastatic tumors from 3 individual patients with the application of Illumina sequencing platform with 150-bp paired-end. Follow-up analyses not only identified differentially expressed genes between different sample sets (a threshold of fold change >2 and adjusted P value <0.05) but also uncovered significantly enriched signaling pathways of individual type. To sum up, our comparative transcriptomic analyses of triple-matched fresh samples stored in liquid nitrogen profiled the molecular expression and revealed functionally enriched pathways underlying the ovarian metastasis of gastric cancer.
2022-06-20 | GSE206329 | GEO
Project description:Metastasis formation is the major cause for cancer-related deaths and the underlying mechanisms remain poorly understood. In this study we describe spontaneous metastasis xenograft mouse models of human neuroblastoma used for unbiased identification of metastasis-related proteins by applying an infrared laser (IR) for sampling primary tumor and metastatic tissues, followed by mass spectrometric proteome analysis. IR aerosol samples were obtained from ovarian and liver metastases, which were indicated by bioluminescence imaging (BLI), and matched subcutaneous primary tumors. Corresponding histology proved the human origin of metastatic lesions. Ovarian metastases were commonly larger than liver metastases indicating differential outgrowth capacities. Among ~1,700 proteins identified at each of the three sites, 89 proteins were differentially regulated in ovarian metastases while 290 proteins were regulated in liver metastases. There was an overlap of 26 and 10 proteins up- and down-regulated at both metastatic sites, respectively, most of which were so far not related to metastasis such as LYPLA2, ACTL8, EIF4B, LGALS7, GFAP, and ELAVL4. Moreover, we established in vitro sublines from primary tumor and metastases and demonstrate differences in cellular protrusions, migratory/invasive potential and glycosylation. Summarized, this work identified several novel putative drivers of metastasis formation that are tempting candidates for future functional studies.
2018-09-24 | PXD009744 | Pride
Project description:Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer related deaths among women in USA. For a comprehensive understanding of the gene expression changes accompanying ovarian carcinogenesis, we isolated RNA from 8 pairs of matched FT and primary tumors from OC patients and sequenced them. Library preparation and next generation RNA sequencing was carried out at the Center for Genomics and Bioinformatics core facility, Indiana University, Bloomington. The library preparation was done using TruSeq Stranded mRNA HT Sample Prep kit (Illumina cat#RS-122-2103) according to the manufacturer’s protocol and 8-neucleotide barcodes were added for multiplexing. The barcoded libraries were cleaned by bead cut with AMPure XP beads (Beckman Coulter, cat#A63882), verified using Qubit3 fluorometer (ThermoFisher Scientific) and 2200 TapeStation bioanalyzer (Agilent Technologies), and then pooled. The pool was sequenced on NextSeq 500 (Illumina) with NextSeq75 High Output v2 kit (Illumina cat#FC-404-2005).
2019-10-18 | GSE137238 | GEO
Project description:Matched high-grade serous ovarian carcinoma samples collected from the ovary (ov), omental metastasis (om-met), and non-omental intraperitoneal metastasis (met) from 10 patients at the time of primary debulking surgery were analyzed for RNA expression by RNA sequencing.
2020-07-02 | GSE133296 | GEO
Project description:BACKGROUND: Ovarian cancer is the most deadly gynecological cancer due to late diagnosis at advanced stage with major peritoneal involvement. To date most research has focused on primary tumor. However the prognosis is directly related to residual disease at the end of the treatment. Therefore it is mandatory to focus and study the biology of metastatic disease that is most frequently localized to the peritoneal cavity in ovarian cancer. METHODS: We used high-density gene expression arrays to investigate gene expression changes between matched primary and metastatic (peritoneal) lesions. RESULTS: Here we show that gene expression profiles in peritoneal metastasis are significantly different than their matched primary tumor and these changes are affected by underlying copy number variation differences among other causes. We show that differentially expressed genes are enriched in specific pathways including JAK/STAT pathway, cytokine signaling and other immune related pathways. We show that underlying copy number variations significantly affect gene expression. Indeed patients with important differences in copy number variation displayed greater gene expression differences between their primary and matched metastatic lesions. CONCLUSIONS: Our analysis shows a very specific targeting at both the genomic and transcriptomic level to upregulate certain pathways in the peritoneal metastasis of ovarian cancer. Moreover, while primary tumors use certain pathways we identify distinct differences with metastatic lesions. The variation between primary and metastatic lesions should be considered in personalized treatment of ovarian cancer.
| S-EPMC3477065 | biostudies-literature
Project description:Transcriptome sequencing of triple-matched samples of gastric cancer patients with ovarian metastasis
| PRJNA850175 | ENA
Project description:Ovarian cancer is the most deadly gynecological cancer. The high rate of mortality is due to the large tumor burden with extensive metastatic lesion of the abdominal cavity. Despite initial chemosensitivity and improved surgical procedures, abdominal recurrence remains an issue and results in patients' poor prognosis. Transcriptomic and genetic studies have revealed significant genome pathologies in the primary tumors and yielded important information regarding carcinogenesis. There are, however, few studies on genetic alterations and their consequences in peritoneal metastatic tumors when compared to their matched ovarian primary tumors. We used high-density SNP arrays to investigate copy number variations in matched primary and metastatic ovarian cancer from 9 patients. Here we show that copy number variations acquired by ovarian tumors are significantly different between matched primary and metastatic tumors and these are likely due to different functional requirements. We show that these copy number variations clearly differentially affect specific pathways including the JAK/STAT and cytokine signaling pathways. While many have shown complex involvement of cytokines in the ovarian cancer environment we provide evidence that ovarian tumors have specific copy number variation differences in many of these genes.
| S-EPMC3237432 | biostudies-literature