Molecular portraits of epithelial, mesenchymal and hybrid states in lung adenocarcinoma and their relevance to survival
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Amin mOMIN
PROVIDER: E-GEOD-63977 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description: Not available
| S-EPMC4846295 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-12-09 | GSE63977 | GEO
Project description:Purpose: There is a quest for novel non-invasive diagnostic markers for the detection of breast cancer. The goal of this study is to identify circulating microRNA signatures using a cohort of Asian Chinese breast cancer patients, and to compare microRNA profiles between tumour and serum samples. Experimental design: MicroRNAs from paired breast cancer tumours, normal tissue and serum samples derived from 32 patients were comprehensively profiled using microarrays (1300 microRNAs against tumour and normal tissues) or LNA RT-PCR panels (742 microRNAs against serum samples). Serum samples from healthy individuals (n=22) were also employed as normal controls. Significant serum microRNAs, identified by logistic regression, were validated in an independent set of serum samples from patients (n=82) and healthy controls (n=53). Results: The 20 most significant microRNAs differentially expressed in breast cancer tumours included miR-21, miR-10b, and miR-145, previously shown to be dysregulated in breast cancer. Interestingly, 16 of the 20 most significant microRNAs differentially expressed in serum samples were novel. MiR-1, miR-92a, miR-133a and miR-133b were identified as the most important diagnostic markers, and were successfully validated; receiver operating characteristic curves derived from combinations of these microRNAs exhibited areas under the curves of 0.944-0.946. Only seven microRNAs were overexpressed in both tumours and serum, suggesting that microRNAs may be released into the serum selectively. Conclusion: The clinical employment of microRNA signatures as a non-invasive diagnostic strategy is promising, but should be further validated for different subtypes of breast cancers. Blood samples were collected in Becton Dickinson (Franklin Lakes, NJ) Vacutainer SST tubes. Serum was harvested by centrifugation at 2200g after allowing blood to clot for 30mins. 32 patient samples and 22 samples from healthy controls were obtained for profiling. Sera samples were stored at -80oC.
2013-09-06 | E-GEOD-41922 | biostudies-arrayexpress
Project description:Sixth generation Exiqon® locked nucleic acid miRCURY™ LNA microarrays were used to profile in duplicate the expression of microRNAs in 250 or 400 ng of RNA isolated from a laser microdissectate of a formalin-fixed and paraffin-embedded human non-small cell lung cancer tumor. Laser microdissection was performed on a hematoxylin-eosin-stained, 8 um-thick section of formalin-fixed and paraffin-embedded tissue. The microdissectate was treated with proteinase K overnight at 55 ºC. Total RNA from the lysate was then extracted using FFPE RNA Isolation Kit from Norgen Biotek® (Thorold, Canada). RiboGreen assay was used to quantify RNA in the preparation. Two-hundred-fifty or 400 ng of RNA was used in duplicate for dual-channel microarray-based microRNA expression profiling. Sample RNA was labeled with the Cy3-like Hy3™ dye, mixed with a human universal reference RNA (product number AM6000, Ambion®, Austin, TX) labeled with the Cy5-like Hy5™ dye, and hybridized to the two-color miRCURY™ arrays.
2011-09-07 | E-GEOD-31946 | biostudies-arrayexpress
Project description:To identify the role of miRNAs in patient bone marrow (BM) and explore the function of these molecules during HCC progression, we employed microarray-based profiling to analyze miRNA expression in the BM of patients with HCC. MicroRNA expression in the BW of HCC patients was measured by using microarray-based profiling. BM cells were separated into 3fraction by cell surface markers as follows: CD45+(macrophage), CD14-/CD45+(lymphocyte) and CD14-/CD45-/EpCAM+(epithelial cell).
2015-08-06 | E-GEOD-71762 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-09-06 | E-GEOD-42128 | biostudies-arrayexpress
Project description:Background: Renal cell carcinoma (RCC) is characterized by a number of diverse molecular aberrations that differ among individuals. Recent approaches to molecularly classify RCC were based on clinical, pathological as well as on single molecular parameters. As a consequence, gene expression patterns reflecting the sum of genetic aberrations in individual tumors may not have been recognized. In an attempt to uncover such molecular features in RCC, we used a novel, unbiased and integrative approach. Methods: We integrated gene expression data from 97 primary RCCs of different pathologic parameters, 15 RCC metastases as well as 34 cancer cell lines for two-way nonsupervised hierarchical clustering using gene groups suggested by the PANTHER Classification System. We depicted the genomic landscape of the resulted tumor groups by means of Single Nuclear Polymorphism (SNP) technology. Finally, the achieved results were immunohistochemically analyzed using a tissue microarray (TMA) composed of 254 RCC. Results: We found robust, genome wide expression signatures, which split RCC into three distinct molecular subgroups. These groups remained stable even if randomly selected gene sets were clustered. Notably, the pattern obtained from RCC cell lines was clearly distinguishable from that of primary tumors. SNP array analysis demonstrated differing frequencies of chromosomal copy number alterations among RCC subgroups. TMA analysis with group-specific markers showed a prognostic significance of the different groups. Conclusion: We propose the existence of characteristic and histologically independent genome-wide expression outputs in RCC with potential biological and clinical relevance. Expression profiling by array, combined data analysis with genomic profiling data. Genomic DNA from renal cell was hybridized to renal cell carcinoma samples and matched normal kidney tissue biopsies, using the Affymetrix GenomewideSNP_6 platform. CEL files were processed using R, Bioconductor and software from the aroma.affymetrix project. Visualized Copy number profiles are accessible through the Progenetix site (www.progenetix.net). CN,raw.csv and segments.csv: Probes are mapped by their position in genome build 36 / HG18. Probes are ordered according to their linear position on the Golden Path.
2012-07-23 | E-GEOD-19949 | biostudies-arrayexpress
Project description: Not available
| S-EPMC1978212 | biostudies-literature
Project description:In this study, the cell wall proteomes of 3 different regions of alfalfa stems were compared. These three regions correspond to three phases in the stem development. The sequential extraction of cell wall proteins with CaCl2, EGTA and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the three proteome patterns are characteristic for each region. In the basal stem region, proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and the apical region are sites of cell wall polymer remodelling, as suggested by the high abundance of proteins involved in the remodelling of the cell wall such as xyloglucan endoglucosylase, polygalacturonase non-catalytic subunit or beta-galactosidase. The most striking change between the different stem parts is however the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem which suggests a particular role of this protein during the early development of stem tissues.
2019-11-12 | PXD010666 | Pride
Project description:Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. We identifed a serum microRNA signature (the miR-Test) that could identify the optimal target population for LDCT screening. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program. RT-qPCR of circulating microRNA purified from serum samples. Trizol-LS and miRNEASY Mini kit (Qiagen) were used for miRNA purification. Custom TaqMan® Low Density Array microRNA Custom Panel (Life Technologies) was used to screen serum circulating microRNA.
2016-02-29 | E-GEOD-76462 | biostudies-arrayexpress