Clear Cell Endometrial Cancer Exome Sequencing Study
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ABSTRACT: The purpose of this study was to identify somatic (tumor-specific) mutations in clear cell endometrial tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 16 de-identified primary tumor DNAs and matched non-tumor DNAs.
SECONDARY ACCESSION(S): PRJNA291461PRJNA291460
REPOSITORIES: dbGaP
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Project description:<p>The purpose of this study was to identify somatic (tumor-specific) mutations in advanced stage endometrioid endometrial carcinoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 19 de-identified primary tumor DNAs, from advanced stage tumors, and matched non-tumor DNAs.</p>
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Project description:<p>Endometrial cancer (EC) is the most commonly diagnosed gynecologic malignancy in the United States and is the sixth leading cause of cancer death amongst American women. The purpose of this study was to identify somatic (tumor-specific) copy number alterations in 7 clear cell ECs, 31 serous ECs, 17 endometrioid ECs, and the clear cell components of 2 endometrioid/clear cell ECs. To this end, DNAs from de-identified primary endometrial tumors and matched non-tumor tissues or blood were hybridized to high-density Illumina Infinium HumanHap650Y Beadchips or to high-density Human660W-Quad Beadchips and the data analyzed to annotate somatic copy number alterations throughout the genome.</p>
| phs001690 | dbGaP
Project description:RNA samples from chicken (Gallus gallus) embryonic fibroblasts (sample ID: ES90) as well as from the HD11 chicken macrophage cell line (sample ID: ES91) were sequenced at the National Institutes of Health Intramural Sequencing Center (NISC) using the Illumina GAIIx technology running the standard CASAVA/ELAND pipeline.
2013-08-01 | E-MTAB-1479 | biostudies-arrayexpress
Project description:The gut-uterus axis plays a pivotal role in the pathogenesis of endometrial cancer (EC). However, the correlations between the endometrial microbiome and endometrial tumor transcriptome in patients with EC and the impact of the endometrial microbiota on hematological indicators have not been thoroughly clarified. In this prospective study, endometrial tissue samples collected from EC patients (n = 30) and healthy volunteers (n = 10) were subjected to 16S rRNA sequencing of the microbiome. The 30 paired tumor and adjacent nontumor endometrial tissues from the EC group were subjected to RNAseq. Result: We found that Pelomonas and Prevotella were enriched in the EC group with a high tumor burden. Further transcriptome analysis identified 8 robust associations between Prevotella and fibrin degradation-related genes expressed within ECs. Conclusions: Our results suggest that the increasing abundance of Prevotella in endometrial tissue combined with high serum DD and FDP contents may be important factors associated with tumor burden.
2021-10-13 | GSE183185 | GEO
Project description:<p>The purpose of the original study was to search for somatic mutations in the tyrosine kinome of serous and clear cell endometrial carcinomas (human). The study was conducted in two phases.</p> <p>Phase 1: A mutation discovery screen, in which ~577 exons encoding the catalytic domains of 86 tyrosine kinases were PCR-amplified and bidirectionally Sanger sequenced from 24 serous, 11 clear cell, and 5 mixed histology endometrial tumors. This was followed by alignment of sequence reads to the human reference sequence and subsequent nucleotide variant calling to identify potential somatic (tumor-specific) mutations. Potential somatic mutations were confirmed by re-amplification and sequencing of the relevant tumor DNA as well as matched non-tumor ("normal") DNA from the same case.</p> <p>Phase 2: A mutation prevalence screen, in which the non-catalytic regions two tyrosine kinase genes, TNK2 and DDR1, were PCR-amplified and sequenced from the 40 discovery screen tumors, and all coding exons of TNK2 and DDR1 were PCR-amplified and sequenced from another 10 clear cell, 21 serous, and 41 endometrioid endometrial tumors, in an effort to identify additional somatic mutations in each gene. Exons encoding the exonuclease domain of POLE were also sequenced to document somatic mutations.</p>
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Project description:Decidualization is critical for the embryonic implantation and successful pregnancy. ATRA can suppress in-vitro decidualization of human endometrial stromal cells (hESCs) induced by MPA and estrogen treatment. However, the mechanism by which RA suppressed estrogen and progesterone induced decidualization of mESCs is not clear. We used microarrays to investigate the mechanism by which all-trans RA (ATRA) regulates the decidualization of endometrial stroma cells (mESCs). mESCs were isolated at day 4 of pseudopregnancy and cultured with administration of E2 and P4 in the presence or absence of ATRA for 72h.
2013-11-05 | E-GEOD-52033 | biostudies-arrayexpress
Project description:Decidualization is critical for the embryonic implantation and successful pregnancy. ATRA can suppress in-vitro decidualization of human endometrial stromal cells (hESCs) induced by MPA and estrogen treatment. However, the mechanism by which RA suppressed estrogen and progesterone induced decidualization of mESCs is not clear. We used microarrays to investigate the mechanism by which all-trans RA (ATRA) regulates the decidualization of endometrial stroma cells (mESCs).
2013-11-05 | GSE52033 | GEO
Project description:Transcriptome profiles were investigated in isolated endometrial stromal cells (ESCs) from eutopic and ectopic endometrium. The profiles were quite different between eutopic ESC and ectopic ESC, whereas no clear dfference was recognized between eutopic ESC with and without endometriosis. Total RNA from three cultured endometrial stromal cells (ESCs) from eutopic endometria without endometriosis, three ESCs with endometriosis and three ESCs from chocolate cysts were hybridised to the Affymetrix Human Gene 1.0 ST Array.
2013-09-07 | E-GEOD-47360 | biostudies-arrayexpress
Project description:Profiles of genome-wide DNA methylation were investigated in isolated endometrial stromal cells from eutopic and ectopic endometrium. DNA methylation profiles were quite different between eutopic ESC and ectopic ESC, whereas no clear dfference were recognized between eutpic ESC with and without endometriosis. Bisulphite converted DNA from three cultured endometrial stromal cells (ESCs) from eutopic endometria without endometriosis, three ESCs with endometriosis and three ESCs from chocolate cysts were hybridised to the Illumina infinium HumanMethylation27 BeadChip.
2013-09-07 | E-GEOD-47359 | biostudies-arrayexpress
Project description:Endometrial cancer (EC) is the most common female genital malignancy and the fourth most common cancer in women in the developing world1. EC has been traditionally classified into two main groups with different clinical, pathological and molecular features2,3. Type I or endometrioid endometrial carcinomas (EECs) account for about 75% of the cases and are typically estrogen-related and low-grade tumors with good prognosis that coexist or are preceded by endometrial hyperplasia, mainly diagnosed in perimenopausal women. In contrast, type II or non-endometrioid endometrial carcinomas (NEECs) are high-grade aggressive tumors associated with endometrial atrophy and poor prognosis, unrelated to estrogen and diagnosed in older women. These comprise several histological subtypes, being the most common the serous carcinomas (SEC)4. In recent years numerous large-scale studies of primary endometrioid and serous tumors have been performed5, revealing new mutated genes and establishing a new molecular subclassification based on the results obtained by The Cancer Genome Atlas (TCGA) consortium6, which implies different clinical outcomes. More recently, the genomic evolution of EC has been analyzed through a comparative study of samples from endometrial atypical hyperplasia, primary tumors and paired metastases7, revealing the presence of intratumor heterogeneity as previously described in primary EC and other tumor types8,9. However an in-depth study considering multiple regions from primary tumor and paired metastases has not been performed up to now to our knowledge. Here we analyze by whole-exome sequencing (WES), massive parallel targeted sequencing and array comparative genomic hybridization (aCGH) the clonal evolution and intratumor heterogeneity of 7 endometrioid and 3 serous metastatic endometrial carcinomas. Different locations from the primary tumor as well as from their paired metastases were included in the study, allowing the reconstruction of the spatial and temporal phylogenetic evolution of the tumor. Different phylogenetic evolution patterns were identified, independently of the classical histological or molecular classification of the tumor, although similar patterns were found in ovarian metastasis and recurrent disease.
2022-02-14 | GSE101447 | GEO