Genomic characterization of five commonly used endometrial cancer cell lines
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE151207 | GEO | 2020/05/27
REPOSITORIES: GEO
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Project description:Genomic characterization of five commonly used endometrial cancer cell lines
| PRJNA635126 | ENA
Project description:Recently, the compilation of massive amounts of genetic and genomic information on a wide variety of human cancer types, collectively known as The Cancer Genome Atlas (TCGA), has revealed a wealth of descriptive classification schemes both within and between different types and sources of cancer. In endometrial cancer, TCGA analyses have produced a post hoc scheme composed of four clusters: DNA polymerase ε catalytic subunit A (POLE) ultra‑mutated (cluster 1), microsatellite instability (MSI) hypermutated (cluster 2), copy‑number low (endometrioid, cluster 3) and copy‑number high (serous‑like, cluster 4). Given that cultured cells are the pre‑clinical platform of cancer research, it was questioned how representative endometrial cancer cultured cell lines are in the context of TCGA‑driven classification scheme. To address this issue in endometrial cancer cell lines, the present study investigated five commonly used cell lines: Ishikawa, ECC‑1, Hec50co, KLE And RL95‑2. The histology, mutation profile, MutL homolog 1 promoter methylation, copy‑number variation, homologous recombination repair and microsatellite instability in each of these cell lines was assessed. The result of this characterization was that none of the cell lines fits neatly into any one of TCGA classes but are still useful models for groups of endometrial tumors. Furthermore, the contention that the ECC‑1 cell line is actually Ishikawa was addressed using additional data. It was confirmed that ECC‑1 cells likely no longer exist as ECC‑1 but that they are not exactly Ishikawa either. For this reason, ECC‑1 cells are suggested to be used in vitro but with this caveat in mind. Finally, we compiled a database of 127 endometrial cancer cell lines, including the five reported on here. The wide range of variation found in these cell lines highlights the need to further characterize these cells to select models that are more representative of the various histological and genomic aspects of endometrial cancer.
| S-EPMC8811471 | biostudies-literature
Project description:Endometrial cancer represents the most frequent gynecologic malignant disease. Although several genetic alterations have been associated with increased risk, to date diagnosis and prognosis still rely on morphological features of the tumor, such as histological type, grading and invasiveness. As molecular-based classification is desirable for optimal treatment and prognosis of these cancers, , we explored the potential of lncRNAs as molecular biomarkers. To this end, we first identified by RNA sequencing (RNA-Seq) a set of lncRNAs differentially expressed in cancer vs normal endometrial tissues, a result confirmed also by analysis of RNA-Seq data of normal and cancerous endometrium from The Cancer Genome Atlas (TCGA). A significant association of a subset of these differentially expressed lncRNAs with tumor grade was then determined in 405 TCGA endometrial cancer profiles. Integrating endometrial cancer-specific expression profiles of long and small non-coding RNAs a functional association network was then identified. These results described for the first time a functional ‘core’ network, comprising small and long RNAs, whose deregulation is associated with endometrial neoplastic transformation, representing a set of cancer biomarkers that can be monitored and targeted for diagnosis, follow-up and therapy of these tumors.
2019-04-30 | E-MTAB-7039 | biostudies-arrayexpress
Project description:<p>Endometrial diseases are common gynecological diseases that disorder women of childbearing age and perimenopausal women, including endometrial polyps (EP), endometrial cancer (EC), and endometrial hyperplasia (EH). Clinically, biopsy or imaging methods are usually used to screen and diagnose endometrial diseases, but due to their invasiveness and heterogeneity, a noninvasive, convenient, objective and accurate biomarker is needed for the differential diagnosis of EP and EC or EH. In the present study, serum samples from 396 patients with endometrial disease and 225 healthy volunteers were analyzed by UPLC-Q-TOF/MS non-targeted lipidomics. A combination of multivariate (Orthogonal partial least-squares discriminant analysis) and univariate (Student t-test) analyses were used to identify and qualify 6, 8, and 7 potential biomarkers in serum from patients with EP, EC, and EH, respectively. With the aid of logistic regression algorithm and receiver operating characteristic (ROC) curve analysis, A biomarker panel including four specific EP biomarkers, 6-Keto-PGF1α, PA(37:4), LysoPC(20:1) and PS (36:0), had good classification and diagnostic ability in distinguishing EP from EC or EH. The biomarker panel can be used as a rapid diagnostic method to assist imaging examination to effectively differentially diagnose endometrial diseases, and provide a reference for clinicians in the identification and diagnosis of endometrial diseases. </p>
2022-01-14 | MTBLS3444 | MetaboLights
Project description:Endometrial cancer is one of the major cancers in women throughout the world. If diagnosed early, these cancers are treatable and the prognosis is usually good. However, one major problem in treating endometrial cancer is accurate diagnosis and staging. Till date, the choice method for diagnosis and staging is histopathology. Although there are few molecular markers identified, they are not always sufficient in making accurate diagnosis and deciding on therapeutic strategy. As a result, very often patients are under treated or over treated. In this study, our group has profiled microRNAs from Indian patients using NGS-based approach. We have identified differentially expressed microRNAs in endometrial cancer. These microRNAs have also been compared to data from TCGA, which represent other populations and also correlated to relevance in overall survival. Using in-silico approaches, mRNA targets of the miRNAs have been predicted. After comparing with TCGA, we have identified 16 miRNA-mRNA pairs which could be potential prognostic biomarkers for endometrial cancer. This is the first miRNA profiling report from Indian cohort and one of the very few studies which have identified potential biomarkers of prognosis in endometrial cancer.
2024-11-13 | GSE268888 | GEO
Project description:Endometrial cancer is the most common gynecological cancer worldwide. In women from developed countries, endometrial cancer is usually detected after the age of 60 years. Nearly 90% of the diagnosed cases are sporadic, while 10% are attributed to genetic factors. Thus, it is necessary to develop a diagnostic platform. Currently, the lymph node status is a major prognostic factor in assessing endometrial cancer. However, despite its high sensitivity, it is still in debate. In order to increase its selectivity and specificity, in-depth proteomic study has been performed on patients sentinel lymph node (SNL) samples and on grade I to grade III endometrial carcinoma (EC) samples. We identified specific markers of bad diagnosis that clearly correlate SNL to EC i.e. PRSS3, PTX3, ASS1, YBX2, RBM25, MUC5B. These markers have also been detected in TCGA. By contrast, we also detected good prognosis markers for the overall survival such as CD74, GOLM1, SLC9A3R2, SP100 proteins. Markers for EC and SNL cancer-grading have also been identified. Taken together, it is now possible to propose a novel approach for molecular diagnosis, prognosis and patient’s stratification in EC which will be of excellent utility in therapeutic decision.
2021-09-09 | PXD020410 | Pride
Project description:IntroductionOrthoses are designed to achieve immobilization or off-loading of certain regions of the foot. Yet, their off-loading capacity for the specific regions has not yet been studied. Therefore, the aim of this study was to analyze the plantar pressure distribution of five commonly applied orthoses for foot and ankle in a healthy population.Materials and methodsFive orthoses (postoperative shoe, forefoot relief shoe, short walker boot, high walker boot, and calcaneus fracture orthosis) were compared pedobarographically using insoles on a treadmill to a ready-made running shoe in eleven healthy subjects (median age 29 years). Peak pressure, maximum force, force-time integral, contact time, and contact area were evaluated separately for the forefoot, midfoot, and hindfoot.ResultsThe forefoot relief shoe, the short- and high walker boot significantly reduced the peak pressure at the forefoot with no significant differences between these orthoses. None of the five orthoses off-loaded the midfoot, but the calcaneus fracture orthosis and the short walker boot instead increased midfoot load. For the hindfoot, the calcaneus fracture orthosis was the only device to significantly reduce the peak pressure.ConclusionsThis is the first study to investigate the specific off-loading capacities of different orthoses for specific foot regions in a healthy collective. The knowledge of absolute and relative load shifts for the different orthoses is of fundamental interest for targeted clinical decision-making of physicians.
| S-EPMC10293377 | biostudies-literature
Project description:Endometrial cancer had a relatively high prevalence of MMR deficiency. MMR-D/MSI-H endometrial cancer patients are suggested to be potential beneficiaries of PD-1/PD-L1 inhibitor therapy. Here, we explored the prognostic value of MSI subtype in endometrial cancer and its correlation with immune environment. Based on expression and clinical data of 78 POLE, 123 MSI and 299 Other EC samples from the TCGA-UCEC project, we found that the MSI tumors were identified more often in early stage, had a lower age, better patient survival, enriched CD8+ T cells, and regulatory T cells and less M2 macrophages and activated dendritic cells than the Other group, and shared a relatively similar expression profile with POLE group by differential analysis. In addition, we established the immune landscape of an MMR-D endometrial cancer tissue using unbiased single-cell RNA-seq analysis of 3371 cells. By immunohistochemistry analysis, we found that the MMR-D tumors showed a higher trend of CD20+ B cells infiltration. Our study might expand our understanding of the role of immune subsets in MSI endometrial carcinomas and provide guidance of immunotherapy for endometrial cancer.
2022-03-09 | GSE193430 | GEO
Project description:We sequenced mRNA of endometrial stromal fibroblasts from six mammalian species. Examination of mRNA levels in endometrial stromal fibroblasts from six mammalian species grown in culture with two biological replicates for each species
2016-08-01 | E-GEOD-67659 | biostudies-arrayexpress