Comparative genomic hybridization of human Merkel cell carcinoma tumors
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Bianca Durando Lemos
PROVIDER: E-GEOD-13239 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Array-CGH profiles of Merkel cell carcinoma tumors Keywords: fresh frozen and formalin fixed paraffin embedded primary tumor, nodal and metastasis merkel cell carcinoma tumor samples
2009-01-01 | GSE13239 | GEO
Project description:Abstract: Purpose: To identify a DNA signature to predict metastasis of small node-negative breast carcinoma Experimental Design: The authors used Comparative Genomic Hybridization (CGH) array to analyze 168 pT1T2pN0 invasive ductal carcinoma patients with either good (no event 5 years after diagnosis: 111 patients) or poor (57 patients with early onset metastasis) outcome. A CGH classifier, identifying low and high-risk groups of metastatic recurrence, was established in a training set of 78 patients. This classifier was based on both genomic regions with statistically different alterations between the two groups of clinical outcome and the number of alterations. It was then tested on a validation set of 90 patients and compared to clinicopathological parameters. Results: The genomic status of regions located on chromosomes 2p22.2, 3p23 and 8q21-24 and the number of segmental alterations were defined in the training set to classify tumors into low or high-risk groups. In the validation set, this CGH classifier produced a highly significant odds ratio of 10.39 (95%CI: 3.75-28.78, p=6.63Ã10-6, Wald test) in univariate analysis with a sensitivity of 66%, a specificity of 84% and an accuracy rate of 78%. The 5-year metastasis-free survival analysis showed a highly significant difference between the two predicted groups (Hazard Ratio=5.7, p=1.82Ã10-7, log-rank test). Together with estrogen receptor and grade, this CGH classifier provided significant prognostic information in multivariate analysis. Conclusions: In addition to classical parameters, this DNA signature may constitute an accurate tool to identify patients with T1T2N0 luminal tumors, who may benefit from adjuvant treatments. Each of the 168 tumoral genomic DNA was hybridized against the same non tumoral DNA reference following identical protocol
2010-05-19 | E-GEOD-19159 | biostudies-arrayexpress
Project description:We performed miRNA expression profiling in a series of human Merkel Cell carcinoma samples using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis. Agilent microarray platform containing 723 human miRNAs was used to determine miRNA expression profiles in 16 human Merkel cell carcinoma (MCC) samples. To validate the microarray platform, the expression levels of selected miRNAs were evaluated using qRT-PCR.
2013-12-31 | E-GEOD-43699 | biostudies-arrayexpress
Project description:Helicobacter pylori strains USU101 was infected into macaques, some of which were treated with the dietary carcinogen ENNG. After 5 years, H. pylori isolates were obtained by endoscopy followed by culture. The resulting strains were analyzed for differences in gene content by array CGH. Array CGH was performed by two color microarray. The monkey output strains were labeled with Cy5 (channel 2) and the input strain USU101 was labeled with Cy3 (channel 1). Each output strain was analyzed by 2-3 separate array experiments.
2014-08-18 | E-GEOD-60405 | biostudies-arrayexpress
Project description:The monkey infecting Helicobacter pylori strain USU101 used in a long term infection of macaques with and without the dietary carcinogen ENNG was analyzed for gene content compared to the sequenced strains 26695 and J99 We performed array CGH using two microarrays to analyze the gene content of the starting strain (USU101) used for the monkey infection experiment (GSE60405). The ENNG information is not relevant.
2014-08-18 | E-GEOD-60404 | biostudies-arrayexpress
Project description:Analysis of changes in gene expression in skin epidermis upon conditional knockout of the essential Polycomb repressive complex 2 (PRC2) subunit Eed. Loss of Eed in skin epithelium leads to de-repression of key Merkel-differentiation genes, which are known PRC2 targets, and results in ectopic formation of Merkel cells that are associated with all hair types. Gene expression analysis: To determine the changes in gene expression in skin epidermis upon conditional knockout of Eed, total RNA was isolated from skin epidermis in four biologic replicates from cells in different conditions and hybridized to SurePrint G3 Mouse GE 8X60K microarrays (Agilent).
2016-06-14 | E-GEOD-83244 | biostudies-arrayexpress
Project description:We superimposed array comparative genomic hybridization (aCGH) data onto existing expression array profiles (GSE3892) to sift out the pivotal genes underlying the pathogenesis of a well defined series of diffuse large B-cell lymphomas (DLBCL). 280 gained and over-expressed genes were identified, located on chromosomes 1q, 3q, 7, 12p12, 18q and 21q. At the most frequently gained region the oncogene MDMX/MDM4 was concurrently over-expressed, which is a critical regulator of p53 function. In regions of frequent chromosomal loss, 36 genes were concurrently down-regulated, restricted to 6q and 15p. These putative tumor suppressor genes included PERP, MAP3K5, CCNDBP1 and β2M, and loss of 6q was associated with poor clinical outcome. Genes identified and chromosomal regions validated in an independent series of DLBCL patients. Overall design fields: Copy number profiles (array CGH) of a series of 42 Diffuse large B-cell lymphoma patient samples were analyzed a) for frequency of aberrations and b) for impact on gene expression. No duplicate samples or dye-swaps were analyzed. a) Statistical analysis of Array CGH data Calling: Areas of gains and losses and their frequencies throughout the dataset were determined from the Bluefuse ratios within the statistical package â??CGHcallâ?? (van de Wiel et al., 2007). Briefly, after smoothing outliers and median normalization, â??DNAcopyâ?? segmentation (Olshen et al., 2004) was applied within CGHcall, after which a call was assigned to each position on the genome. Within CGHcall the probabilities of the calls were determined per chromosomal arm, and a cellularity correction of 0.75 was applied to each sample because tumor cellularity in all DLBCL is estimated to be maximal 75%, taking into account all stromal, endothelial en infiltrating lymphocytes. After calling, we applied â??CGHregionsâ?? (van de Wiel and van Wieringen 2007) to determine regions of consecutive clones with highly similar calls for all samples. This dimension reduction further increases robustness and statistical power for downstream statistical analyses. Called data were used for all downstream analyses. b) Integration with expression data To integrate called array CGH data with expression array data, the array CGH and expression integration tool, ACE-it (van Wieringen et al., 2006), was used. For ACE-it analysis chromosomal amplifications were included in the gains. ACE-it uses the one-sided Wilcoxon rank sum to test which chromosomal aberrations recurrently affect RNA expression and adjust p-values for multiple testing. Only those clones were taken into account which had at least 20% (9) of the samples in one of the other calling states (gain or loss). Only genes were considered relevant with a false discovery rate of <0.1. References - Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-72. - van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN, Wilting SM, Ylstra B (2007) CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics 23: 892-4. - van de Wiel MA, van Wieringen WN. CGHregions: dimension reduction for array CGH data with minimal information loss. Cancer Informatics. In press 2007. - van Wieringen WN, Belien JA, Vosse SJ, Achame EM, Ylstra B (2006) ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics 22: 1919-20.
2010-06-25 | E-GEOD-5138 | biostudies-arrayexpress
Project description:A better understanding of the consequences of recurrent (epi)genetic alterations that occur during cervical carcinogenesis is essential in the search for novel biomarkers. In this study we determined genome-wide expression profiles of 10 squamous cell carcinomas (SCCs), 5 adenocarcinomas (AdCAs) and 6 normal epithelial samples. Expression patterns were subsequently combined with previously determined chromosomal profiles in the same carcinomas. Differential gene expression analysis identified 76 genes with altered expression in carcinomas compared to normal epithelium. Microarray results for a subset of these genes were validated by real-time RT-PCR. Among the differentially expressed genes a relative overrepresentation of genes located at chromosome 3q, one of the most frequently gained areas in SCCs, was observed (false discovery rate (FDR)<0.005). To further investigate the relationship between gene expression and chromosomal alterations 2 statistical approaches were used, i.e. differential gene locus mapping (DIGMAP) and the array CGH expression integration tool (ACE-it). Using these methods we found that increased gene expression was linked to increased gene copy numbers at 1q32.1, 3q13.32-22.3, 3q26.32-27.3, and 20q11.21-13.33, whereas a loss at 11q22.3-25 correlated with recurrent decreased gene expression. Integrated genome-wide chromosomal and transcriptional analysis of cervical carcinomas highlighted 7 genes (i.e. FLJ21291, DTX3L, CCDC14, MCM2, PIK3R4, ATP2C1 and SLC25A36), which were identified by differential gene expression analysis and were located within the chromosomal regions identified by DIGMAP and/or ACE-it as well. Further investigations of these promising marker genes in warranted. Keywords: microarray analysis, array CGH, cervical cancer For microarray mRNA expression analysis 10 SCCs, 5 AdCAs and 6 normal epithelial controls were used. Normal cervical controls consisted of 1 pool of 3 normal cervices distant from tumour, 1 pool of 4 normal ectocervical smears and 1 pool of 5 normal endocervical smears. To expand our number of normal squamous epithelial controls, we included expression profiles of 3 uvulas of non-cancer patients who underwent uvulopalatopharyngoplasty. In addition, we hybridised RNA isolated from 2 different biopsies of the same SCC (SCC12 and SCC13) as a biological replicate. The pool of 4 normal ectocervical smears was hybridised twice as a technical replicate to determine technical variation. Genomic profiling of the same 10 SCCs and 5 AdCAs was done using array CGH (Wilting et al, J Pathol 2006, volume 209, p 220-30).
2010-06-25 | E-GEOD-6473 | biostudies-arrayexpress
Project description:Primary diffuse large B cell lymphomas of different immune-privileged sites (IP-DLBCL) share many clinical and biological features, such as a relatively poor prognosis, preferential dissemination to other immune-privileged sites and deletion of the HLA region, which suggests that IP-DLBCL represents a separate entity. To further investigate the nature of IP-DLBCL, we investigated site-specific genomic aberrations in 16 testicular, 9 central nervous system (CNS) and 15 nodal DLBCL using array-CGH. We also determined minimal common regions of gain and loss. Using robust algorithms, the array-CGH data were combined with gene expression data to explore pathways deregulated by chromosomal aberrations. Keywords: comparative genomic hybridisation, gene expression, tumor type comparison Whole tissue sections of 16 testicular, 9 central nervous system (CNS) and 15 nodal DLBCL were used for isolation of genomic DNA and total RNA. Genomic aberrations were determined using an in house printed CGH array containing ~3700 large genomic insert clones. Gene expression was analyzed on Affymetrix HU133 plus 2.0 oligo arrays. Gene expression data and arrayCGH data were combined using the R program ACE-it.
2008-06-18 | E-GEOD-10524 | biostudies-arrayexpress
Project description:Fibrillin-1 (FBN1) is the major component of extracellular matrix microfibrils, which are required for proper development of elastic tissues including heart and lung. Through protein-protein interactions with latent TGF-beta binding protein 1 (LTBP1), microfibrils assist regulation of TGF-beta signaling. Mutations within the 47 epidermal growth factor-like (EGF) repeats of FBN1 cause autosomal dominant disorders including Marfan Syndrome that disrupt TGF-beta signaling. We recently identified 2 novel protein O-glucosyltransferases, Protein O-glucosyltransferase 2 (POGLUT2) and Protein O-glucosyltransferase 3 (POGLUT3), that modify a few EGF repeats on Notch. Here, using mass spectral analysis, we show that POGLUT2 and POGLUT3 also modify over half of the EGF repeats on FBN1, fibrillin-2 (FBN2), and LTBP1. While most sites are modified by both enzymes, some sites show a preference for either POGLUT2 or POGLUT3. POGLUT2 and POGLUT3 are homologs of POGLUT1, which stabilizes Notch proteins by addition of O-glucose to Notch EGF repeats. Like POGLUT1, POGLUT2 and 3 can discern a folded versus unfolded EGF repeat, suggesting POGLUT2 and 3 are involved in a protein folding pathway. In vitro secretion assays using recombinant FBN1 revealed reduced FBN1 secretion in POGLUT2 knockout, POGLUT3 knockout, and POGLUT2 and 3 double knockout HEK293T cells compared to wild type. These results illustrate that POGLUT2 and 3 function together to O-glycosylate protein targets, and that these modifications play a role in secretion of target proteins.
2021-08-06 | PXD025725 | Pride