Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Cunliffe Heather
PROVIDER: S-ECPF-GEOD-49888 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Transcriptional profiling of 19 ovarian tumors of 5 distinct histologic types (serous, endometrioid, clear cell, mucinous and small cell), to investigate similar and distinct biology associated with each histologic type. RNA from fresh-frozen ovarian tumor samples were individually hybridized to a pooled RNA from all 19 tumor cases
2014-01-17 | E-GEOD-49888 | biostudies-arrayexpress
Project description:Transcriptional profiling of 19 ovarian tumors of 5 distinct histologic types (serous, endometrioid, clear cell, mucinous and small cell), to investigate similar and distinct biology associated with each histologic type.
2014-01-17 | GSE49888 | GEO
Project description:BackgroundWe previously identified a number of genes which were methylated significantly more frequently in the tumor compared to the non-cancerous lung tissues from non-small cell lung cancer (NSCLC) patients. Detection of methylation profiles of genes in NSCLC could provide insight into differential pathways to malignancy and lead to strategies for better treatment of individuals with NSCLC.MethodsWe determined the DNA methylation status of 27 genes using quantitative MethyLight assays in lung tumor samples from 117 clinically well-characterized NSCLC patients.ResultsHypermethylation was detected in one of more of the genes in 106 (91%) of 117 cases and was detected at high levels (percentage methylation reference (PMR)> or =4%) in 79% of NSCLC cases. Methylation of APC, CCND2, KCNH5 and, RUNX was significantly more frequent in adenocarcinomas compared to squamous cell carcinomas (SCC), while methylation of CDKN2A was more common in SCC. Hypermethylation of KCNH5, KCNH8, and RARB was more frequent in females compared to males. Hypermethylation of APC and CCND2 was inversely associated with proliferation score assessed by Ki-67 level.ConclusionsOur findings of differential gene hypermethylation frequencies in tumor tissues from patients with adenocarcinoma or squamous cell cancers and in females compared to males suggests that further investigation is warranted in order to more fully understand the potential disparate pathways and/or risk factors for NSCLC associated with histologic type and gender.
| S-EPMC2888601 | biostudies-literature
Project description:Transcriptional profiling of human lung minimally invasive adenocarcinoma cells comparing control lepidic growth (LG) cell pool with micro-invasion (MI) cell pool. Two-condition experiment, LG vs. MI cell pools. Biological replicates: 1 control LG cancer cell, 1 MI cancer cell in an individual MIA tumor. One replicate per array.
| S-ECPF-GEOD-30663 | biostudies-other
Project description:BackgroundPrevious results obtained from serum samples of late-stage, high-grade serous ovarian carcinoma patients showed large alterations in lipid metabolism. To validate and extend the results, we studied lipidomic changes in early-stage ovarian tumours. In addition to serous ovarian cancer, we investigated whether these changes occur in mucinous and endometrioid histological subtypes as well.MethodsAltogether, 354 serum or plasma samples were collected from three centres, one from Germany and two from Finland. We performed lipidomic analysis of samples from patients with malignant (N = 138) or borderline (N = 25) ovarian tumours, and 191 controls with benign pathology. These results were compared to previously published data.ResultsWe found 39 lipids that showed consistent alteration both in early- and late-stage ovarian cancer patients as well as in pre- and postmenopausal women. Most of these changes were already significant at an early stage and progressed with increasing stage. Furthermore, 23 lipids showed similar alterations in all investigated histological subtypes.ConclusionsChanges in lipid metabolism due to ovarian cancer occur in early-stage disease but intensify with increasing stage. These changes occur also in other histological subtypes besides high-grade serous carcinoma. Understanding lipid metabolism in ovarian cancer may lead to new therapeutic and diagnostic alternatives.
| S-EPMC6189177 | biostudies-literature
Project description:Gene fusions play a critical role in some cancers and can serve as important clinical targets. In epithelial ovarian cancer (EOC), the contribution of fusions, especially by histological type, is unclear. We therefore screened for recurrent fusions in a histologically diverse panel of 220 EOCs using RNA sequencing. The Pipeline for RNA-Sequencing Data Analysis (PRADA) was used to identify fusions and allow for comparison with The Cancer Genome Atlas (TCGA) tumors. Associations between fusions and clinical prognosis were evaluated using Cox proportional hazards regression models. Nine recurrent fusions, defined as occurring in two or more tumors, were observed. CRHR1-KANSL1 was the most frequently identified fusion, identified in 6 tumors (2.7% of all tumors). This fusion was not associated with survival; other recurrent fusions were too rare to warrant survival analyses. One recurrent in-frame fusion, UBAP1-TGM7, was unique to clear cell (CC) EOC tumors (in 10%, or 2 of 20 CC tumors). We found some evidence that CC tumors harbor more fusions on average than any other EOC histological type, including high-grade serous (HGS) tumors. CC tumors harbored a mean of 7.4 fusions (standard deviation [sd] = 7.4, N = 20), compared to HGS EOC tumors mean of 2.0 fusions (sd = 3.3, N = 141). Few fusion genes were detected in endometrioid tumors (mean = 0.24, sd = 0.74, N = 55) or mucinous tumors (mean = 0.25, sd = 0.5, N = 4) tumors. To conclude, we identify one fusion at 10% frequency in the CC EOC subtype, but find little evidence for common (> 5% frequency) recurrent fusion genes in EOC overall, or in HGS subtype-specific EOC tumors.
| S-EPMC5564530 | biostudies-literature
Project description:Internationally, ovarian cancer is the 7th leading cancer diagnosis and 8th leading cause of cancer mortality among women. Ovarian cancer incidence varies by region, particularly when comparing high vs. low-income countries. Temporal changes in reproductive factors coupled with shifts in diagnostic criteria may have influenced incidence trends of ovarian cancer and relative rates by histologic subtype. Accordingly, we evaluated trends in ovarian cancer incidence overall (1973-1977 to 2003-2007) and by histologic subtype (1988-1992 to 2003-2007) using volumes IV-IX of the Cancer Incidence in Five Continents database (CI5plus) and CI5X (volume X) database. Annual percent changes were calculated for ovarian cancer incidence trends, and rates of histologic subtypes for individual countries were compared to overall international incidence. Ovarian cancer incidence rates were stable across regions, although there were notable increases in Eastern/Southern Europe (e.g., Poland: Annual Percent Change (APC) 1.6%, p = 0.02) and Asia (e.g., Japan: APC 1.7%, p = 0.01) and decreases in Northern Europe (e.g., Denmark: APC -0.7%, p = 0.01) and North America (e.g., US Whites: APC -0.9%, p < 0.01). Relative proportions of histologic subtypes were similar across countries, except for Asian nations, where clear cell and endometrioid carcinomas comprised a higher proportion of the rate and serous carcinomas comprised a lower proportion of the rate than the worldwide distribution. Geographic variation in temporal trends of ovarian cancer incidence and differences in the distribution of histologic subtype may be partially explained by reproductive and genetic factors. Thus, histology-specific ovarian cancer should continue to be monitored to further understand the etiology of this neoplasm.
| S-EPMC5595147 | biostudies-literature
Project description:BackgroundAfter a period of increasing rates, lung cancer incidence is declining in the US for men and women. We investigated lung cancer rate patterns by gender, geographic location, and histologic subtype, and for total lung cancer (TLC), for the entire study period, and for 2000-2011 from 17 surveillance, epidemiology, and end results areas.MethodsFor each gender-histologic type combination, time trend plots and maps of age-adjusted rates are presented. Time trend significance was tested by joinpoint regression analysis. Spatial random effects models were applied to examine effects of sociodemographic factors, health insurance coverage, smoking, and physician density at the county level. Linked micromap plots illustrate patterns for important model predictors.ResultsDeclining incidence trends occurred for TLC (p < 0.05, entire period). Squamous cell carcinoma trends increased for females only (p < 0.05). Small cell carcinoma trends declined overall, p < 0.05, but recently increased faster for females than males. Adenocarcinoma rates initially declined, but were significantly increasing by 2004, p < 0.05. Counties with higher current smoking and family poverty were strongly associated with higher risk for all gender-histologic types (p < 0.0001, for both variables). County socioeconomic status was associated with higher risk for all lung cancer subtypes for females, p < 0.02. Counties with more diagnostic radiologists were associated with higher TLC rates (p < 0.03); counties with greater primary care physician access were associated with lower TLC rates (p < 0.03). TLC incidence rates were higher in eastern and southern states than western areas. Male rates were higher than female rates along the West Coast. Males and females had similar small cell rate patterns, with higher rates in the Midwest and southeast. Squamous cell carcinoma and adenocarcinoma rate patterns were similar to TLC patterns, except for relatively higher female adenocarcinoma rates in the northeast and northwest.ConclusionGeographic patterns and declining time trends for incident lung cancer are consistent with previous mortality patterns. Male-female time trend and geographic pattern differences occur by histologic type. Time trends remain significant, even after adjustment for significant covariates. Knowledge of the variation of lung cancer incidence by region and histologic type is useful for surveillance and for implementing lung cancer control efforts.
| S-EPMC5437205 | biostudies-literature
Project description:Whether risk factors for epithelial ovarian cancer (EOC) differ by subtype (i.e., dualistic pathway of carcinogenesis, histologic subtype) is not well understood; however, data to date suggest risk factor differences. We examined associations between reproductive and hormone-related risk factors for EOC by subtype in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Among 334,126 women with data on reproductive and hormone-related risk factors (follow-up: 1992-2010), 1,245 incident cases of EOC with known histology and invasiveness were identified. Data on tumor histology, grade, and invasiveness, were available from cancer registries and pathology record review. We observed significant heterogeneity by the dualistic model (i.e., type I [low grade serous or endometrioid, mucinous, clear cell, malignant Brenner] vs. type II [high grade serous or endometrioid]) for full-term pregnancy (phet ?=?0.02). Full-term pregnancy was more strongly inversely associated with type I than type II tumors (ever vs. never: type I: relative risk (RR) 0.47 [95% confidence interval (CI): 0.33-0.69]; type II, RR: 0.81 [0.61-1.06]). We observed no significant differences in risk in analyses by major histologic subtypes of invasive EOC (serous, mucinous, endometrioid, clear cell). None of the investigated factors were associated with borderline tumors. Established protective factors, including duration of oral contraceptive use and full term pregnancy, were consistently inversely associated with risk across histologic subtypes (e.g., ever full-term pregnancy: serous, RR: 0.73 [0.58-0.92]; mucinous, RR: 0.53 [0.30-0.95]; endometrioid, RR: 0.65 [0.40-1.06]; clear cell, RR: 0.34 [0.18-0.64]; phet ?=?0.16). These results suggest limited heterogeneity between reproductive and hormone-related risk factors and EOC subtypes.
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Project description:Further characterization of thymic epithelial tumors (TETs) is needed. Genomic information from 102 evaluable TETs from The Cancer Genome Atlas (TCGA) dataset and from the IU-TAB-1 cell line (type AB thymoma) underwent clustering analysis to identify molecular subtypes of TETs. Six novel molecular subtypes (TH1-TH6) of TETs from the TCGA were identified, and there was no association with WHO histologic subtype. The IU-TAB-1 cell line clustered into the TH4 molecular subtype and in vitro testing of candidate therapeutics was performed. The IU-TAB-1 cell line was noted to be resistant to everolimus (mTORC1 inhibitor) and sensitive to nelfinavir (AKT1 inhibitor) across the endpoints measured. Sensitivity to nelfinavir was due to the IU-TAB-1 cell line's gain-of function (GOF) mutation in PIK3CA and amplification of genes observed from array comparative genomic hybridization (aCGH), including AURKA, ERBB2, KIT, PDGFRA and PDGFB, that are known upregulate AKT, while resistance to everolimus was primarily driven by upregulation of downstream signaling of KIT, PDGFRA and PDGFB in the presence of mTORC1 inhibition. We present a novel molecular classification of TETs independent of WHO histologic subtype, which may be used for preclinical validation studies of potential candidate therapeutics of interest for this rare disease.
| S-EPMC8202771 | biostudies-literature