scholarly journals On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles

2013 ◽  
Author(s):  
Ying-Wooi Wan ◽  
Claire Mach ◽  
Genevera I. Allen ◽  
Matthew Anderson ◽  
Zhandong Liu
Keyword(s):  
Ovarian Cancer ◽  
Cancer Survival ◽  
Human Cancer ◽  
The Cancer Genome Atlas ◽  
Detection Algorithms ◽  
Level 3 ◽  
Cancer Genome Atlas ◽  
Ovarian Cancer Survival ◽  
Generation Sequencing

Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that are associated with survival when miRNAs were profiled in the same specimens using Next Generation Sequencing (miRNA-Seq) (p<0.01). Surprisingly, only 1 miRNA transcript is associated with ovarian cancer survival in both datasets. Our analyses indicate that this discrepancy is due to the fact that miRNA levels reported by the two platforms correlate poorly, even after correcting for potential issues inherent to signal detection algorithms. Further investigation is warranted.

Clinical translation of the cancer genome atlas signature for ovarian cancer survival

2012 ◽  
Vol 125 ◽  
pp. S42
Author(s):  
G. Sfakianos ◽  
E. Iversen ◽  
W. Lowery ◽  
R. Whitaker ◽  
L. Akushevich ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Survival ◽  
Cancer Genome ◽  
Clinical Translation ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Ovarian Cancer Survival ◽  
Genome Atlas

scholarly journals Comprehensive Analysis of The Significance of Hypoxia-Related Genes in Ovarian Cancer

2021 ◽  
Author(s):  
Wancheng Zhao ◽  
Lili Yin
Keyword(s):  
Ovarian Cancer ◽  
Epithelial Mesenchymal Transition ◽  
Principal Component ◽  
Vital Role ◽  
The Cancer Genome Atlas ◽  
Consensus Clustering ◽  
Mesenchymal Transition ◽  
Cancer Genome Atlas ◽  
Pca Algorithm

Abstract Background: Hypoxia-related genes have been reported to play important roles in a variety of cancers. However, their roles in ovarian cancer (OC) have remained unknown. The aim of our research was to explore the significance of hypoxia-related genes in OC patients.Methods: In this study, 15 hypoxia-related genes were screened from The Cancer Genome Atlas (TCGA) database to group the ovarian cancer patients using the consensus clustering method. Principal component analysis (PCA) was performed to calculate the hypoxia score for each patient to quantify the hypoxic status. Results: The OC patients from TCGA-OV dataset were divided into two distinct hypoxia statuses (cluster.A and cluster.B) based on the expression level of the 15 hypoxia-related genes. Most hypoxia-related genes were expressed more highly in the cluster.A group than in the cluster.B group. We also found that patients in the cluster.A group exhibited higher expression of immune checkpoint-related genes, epithelial-mesenchymal transition-related genes, and immune activation-related genes, as well as elevated immune infiltrates. PCA algorithm indicated that patients in the cluster.A group had higher hypoxia scores than that in in the cluster.B group.Conclusions: In summary, our research elucidated the vital role of hypoxia-related genes in immune infiltrates of OC. Our investigation of hypoxic status may be able to improve the efficacy of immunotherapy for OC.

Role of hypertension associated genes with ovarian cancer survival in the TCGA data.

2012 ◽  
Vol 125 ◽  
pp. S38
Author(s):  
S. Hensley Alford ◽  
J. Li ◽  
X. Yang ◽  
T. Buekers ◽  
A. Munkarah
Keyword(s):  
Ovarian Cancer ◽  
Cancer Survival ◽  
Ovarian Cancer Survival

The role of glutathione-S-transferase polymorphisms in ovarian cancer survival

2007 ◽  
Vol 43 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Christina M. Nagle ◽  
Georgia Chenevix-Trench ◽  
Amanda B. Spurdle ◽  
Penelope M. Webb
Keyword(s):  
Ovarian Cancer ◽  
Cancer Survival ◽  
Glutathione S Transferase ◽  
Ovarian Cancer Survival

scholarly journals In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses

2021 ◽  
Vol 22 (3) ◽  
pp. 1097
Author(s):  
Jeong Hoon Lee ◽  
Kye Hwa Lee ◽  
Ju Han Kim
Keyword(s):  
Cancer Survival ◽  
Human Cancer ◽  
Survival Rates ◽  
Cumulative Effect ◽  
Suppressor Gene ◽  
The Cancer Genome Atlas ◽  
Prognostic Effect ◽  
Ic50 Values ◽  
Cancer Genome Atlas ◽  
Tp53 Tumor Suppressor Gene

To exploit negatively interacting pairs of cancer somatic mutations in chemotherapy responses or synthetic cytotoxicity (SC), we systematically determined mutational pairs that had significantly lower paclitaxel half maximal inhibitory concentration (IC50) values. We evaluated 407 cell lines with somatic mutation profiles and estimated their copy number and drug-inhibitory concentrations in Genomics of Drug Sensitivity in Cancer (GDSC) database. The SC effect of 142 mutated gene pairs on response to paclitaxel was successfully cross-validated using human cancer datasets for urogenital cancers available in The Cancer Genome Atlas (TCGA) database. We further analyzed the cumulative effect of increasing SC pair numbers on the TP53 tumor suppressor gene. Patients with TCGA bladder and urogenital cancer exhibited improved cancer survival rates as the number of disrupted SC partners (i.e., SYNE2, SON, and/or PRY) of TP53 increased. The prognostic effect of SC burden on response to paclitaxel treatment could be differentiated from response to other cytotoxic drugs. Thus, the concept of pairwise SC may aid the identification of novel therapeutic and prognostic targets.

scholarly journals ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

2020 ◽  
Vol 19 (12) ◽  
pp. 2115-2124 ◽  
Author(s):  
Johannes Griss ◽  
Guilherme Viteri ◽  
Konstantinos Sidiropoulos ◽  
Vy Nguyen ◽  
Antonio Fabregat ◽  
...  
Keyword(s):  
B Cell ◽  
Plasma Cells ◽  
Human Cancer ◽  
The Cancer Genome Atlas ◽  
The Novel ◽  
Specific Subset ◽  
Public Data ◽  
Cancer Genome Atlas ◽  
Pathway Analyses

Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge.Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactome's existing web interface and the novel ReactomeGSA R Bioconductor package with explicit support for scRNA-seq data. Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis. ReactomeGSA greatly reduces the technical barrier for multi-omics, cross-species, comparative pathway analyses.We used ReactomeGSA to characterize the role of B cells in anti-tumor immunity. We compared B cell rich and poor human cancer samples from five of the Cancer Genome Atlas (TCGA) transcriptomics and two of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteomics studies. B cell-rich lung adenocarcinoma samples lacked the otherwise present activation through NFkappaB. This may be linked to the presence of a specific subset of tumor associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma. This showcases how ReactomeGSA can derive novel biomedical insights by integrating large multi-omics datasets.

scholarly journals HNRNPH1-stabilized LINC00662 promotes ovarian cancer progression by activating the GRP78/p38 pathway

Oncogene ◽  
2021 ◽  
Author(s):  
Yong Wu ◽  
Qinhao Guo ◽  
Xingzhu Ju ◽  
Zhixiang Hu ◽  
Lingfang Xia ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Progression ◽  
Prognostic Indicator ◽  
Mapk Signaling ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Proliferation And Metastasis ◽  
Nuclear Ribonucleoprotein

AbstractNumerous studies suggest an important role for copy number alterations (CNAs) in cancer progression. However, CNAs of long intergenic noncoding RNAs (lincRNAs) in ovarian cancer (OC) and their potential functions have not been fully investigated. Here, based on analysis of The Cancer Genome Atlas (TCGA) database, we identified in this study an oncogenic lincRNA termed LINC00662 that exhibited a significant correlation between its CNA and its increased expression. LINC00662 overexpression is highly associated with malignant features in OC patients and is a prognostic indicator. LINC00662 significantly promotes OC cell proliferation and metastasis in vitro and in vivo. Mechanistically, LINC00662 is stabilized by heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1). Moreover, LINC00662 exerts oncogenic effects by interacting with glucose-regulated protein 78 (GRP78) and preventing its ubiquitination in OC cells, leading to activation of the oncogenic p38 MAPK signaling pathway. Taken together, our results define an oncogenic role for LINC00662 in OC progression mediated via GRP78/p38 signaling, with potential implications regarding therapeutic targets for OC.

Vaginal hysterectomy with or without bilateral salpingo-oophorectomy may be an alternative treatment for endometrial cancer patients with medical co-morbidities precluding standard surgical procedures: a systematic review

2019 ◽  
Vol 29 (2) ◽  
pp. 299-304 ◽  
Author(s):  
Arnold-Jan Kruse ◽  
Henk G ter Brugge ◽  
Harm H de Haan ◽  
Hugo W Van Eyndhoven ◽  
Hans W Nijman
Keyword(s):  
Ovarian Cancer ◽  
Endometrial Cancer ◽  
Vaginal Hysterectomy ◽  
Cancer Survival ◽  
Survival Rates ◽  
Survival Outcomes ◽  
Ovarian Malignancy ◽  
Post Menopausal ◽  
Ovarian Cancer Survival ◽  
Overall Survival Rates

ObjectiveVaginal hysterectomy with bilateral salpingo-oophorectomy may be an alternative strategy for patients with low-risk endometrial cancer and medical co-morbidities precluding laparoscopic or abdominal procedures. The current study evaluates the prevalence of co-existent ovarian malignancy in patients with endometrial cancer and the influence of bilateral salpingo-oophorectomy on survival outcomes in these patients.MethodsMedline and EMBASE were searched for studies published between January 1, 2000 and November 20, 2017 that investigated (1) the prevalence of co-existing ovarian malignancy (either metastases or primary synchronous ovarian cancer in women with endometrial cancer, and (2) the influence of bilateral salpingo-oophorectomy on recurrence and/or survival rates.ResultsOf the pre-menopausal and post-menopausal patients (n=6059), 373 were identified with metastases and 106 were identified with primary synchronous ovarian cancer. Of the post-menopausal patients (n=6016), 362 were identified with metastases and 44 were identified with primary synchronous ovarian cancer. Survival outcomes did not differ for pre-menopausal patients with endometrial cancer with and without bilateral salpingo-oophorectomy (5-year overall survival rates were 89–94.5% and 86–97.8%, respectively).ConclusionBilateral salpingo-oophorectomy during vaginal hysterectomy seems to have a limited impact on disease outcome in patients with endometrial cancer. These results support the view that vaginal hysterectomy alone or with bilateral salpingo-oophorectomy may be an option for patients with endometrial cancer who are not ideal surgical candidates.

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