RNA profiling from ovarian and prostate FFPE specimens
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Svitlana Tyekucheva
PROVIDER: E-GEOD-54809 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. We profiled seven paired tumor and adjacent normal prostate tissue samples from three patients with Gleason score 8, one with Gleason score 7 and three with Gleason 6 disease. 11 samples had two or three technical replicates.
2014-07-01 | E-GEOD-54808 | biostudies-arrayexpress
Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. five paired tumor and adjacent normal prostate tissue speciemens with technical replicates
2014-07-01 | E-GEOD-55055 | biostudies-arrayexpress
Project description:Overall paediatric high grade glioma (pHGG) has a poor prognosis, in part due to the lack of understanding of the underlying biology. We therefore used high resolution 244k oligo array comparative genomic hybridisation (oligo aCGH) (Agilent Technologies) to analyse DNA from 38 formalin-fixed paraffin embedded pHGG samples, including 13 DIPG (ten pre-treatment samples and three post-mortem). The pattern of gains and losses were distinct from those seen in HGG arising in adults. In particular we found 1q gain in 22% of our cohort compared to 9% in adults. Homozygous loss at 8p12 was seen in 6/38 (15%) of pHGG. This deletion has not been previously reported in adult or paediatric high grade gliomas. The minimal deleted region is of the gene ADAM3A and homozygous deletion of ADAM3A was confirmed by quantitative real time PCR (qPCR). This novel homozygous deletion of ADAM3A in pHGG merits further study. Loss of CDKN2A/CDKN2B was seen in 4/38 (10%) samples by oligo a CGH, confirmed by FISH on TMAs and was restricted to supratentorial tumours. Amplification of the 4q11-13 region was detected in 8% of cases and included PDGFRA and KIT, subsequent qPCR analysis was consistent with amplification of PDGFRA. MYCN amplification was seen in 2/38 samples (5%) and was shown to be significantly associated with anaplastic astrocytomas (p=0.03). Overall DIPG shared similar spectrum of changes to supratentorial HGG with some notable differences including high frequency of 17p loss and 14q loss and lack of CDKN2A/CDKN2B deletion. To our knowledge, this study examines the largest DIPG cohort to date using high-throughput genetic techniques. 38 high grade glioma samples including 13 DIPG (ten pre-treatment samples and three post-mortem) analysed by Agilent 244K array CGH. Samples BSG 1, 2, 3, 5, 6, 7, 8, 9, 10 and 11 are the ten pre-treatment DIPG samples. Samples BSG 4, 12 and 13 are the three post-treatment DIPG samples.
2010-12-01 | E-GEOD-21420 | biostudies-arrayexpress
Project description:Background Despite improvement in diagnostic and therapeutic techniques, a significant percentage of patients with early stage laryngeal cancer still recur after treatment. Gene expression models prognostic of recurrence risk could suggest which patients with early stage laryngeal cancer would be more appropriate for testing adjuvant strategies. Patients and Methods Expression profiling using whole genome DASL arrays was performed on 56 formalin-fixed paraffin-embedded tumor samples of patients with early stage laryngeal cancer, treated with surgery or radiation therapy. We split the samples into a training set and a validation set. Using the supervised principal components survival analysis in the first cohort, we identified multiple gene expression profiles that predict the risk of recurrence. These profiles were then validated in the second independent cohort. Results Gene models comprising different number of genes (40-100) identified a subgroup of patients who were at high risk of recurrence. Of these, the best prognostic model distinguished between a high- and a low-risk group (median DFS: 92 and 123 months, log rank p<0.005, permutation p<0.05), Hazard Ratio (HR): 8.51 (95% CI, 1.01 to 71.77; p<0.05). These models performed similarly in the independent cohort of our study (median DFS: 38 vs 161 months, log rank p=0.018), HR=5.19 (95% CI, 1.14 to 23.57; p<0.05). Conclusions We have identified gene expression prognostic models which can refine the estimation of a patient’s risk of recurrence. These findings, if further validated, should aid in patient stratification for testing adjuvant treatment strategies. 56 patients with early stage laryngeal cancer were included in this study.
2011-11-26 | E-GEOD-25727 | biostudies-arrayexpress
Project description:Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.
2023-10-02 | PXD045840 | Pride
Project description:To investigate mechanisms involved in the dysplastic progression of SSA, we evaluated differential expressions of mRNAs between areas with and without dysplasia within same SSA polyps.
2019-05-18 | E-MTAB-7960 | biostudies-arrayexpress
Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.
2015-02-18 | E-MTAB-2914 | biostudies-arrayexpress
Project description:Neuroendocrine neoplasms of the gallbladder and liver occur rarely in dogs and humans. A recent reclassification of human neuroendocrine neoplasms by the World Health Organization has refined categorization of these tumors by morphology, replicative indices, and molecular signatures. In humans, these factors correlate with survival outcomes. Improved characterization of these tumors is needed in dogs to identify diagnostic biomarkers and determine therapeutic strategies. To achieve this objective, the proteome of 3 canine hepatobiliary neoplasms was compared to normal canine adrenal and liver tissue from formalin-fixed paraffin-embedded samples. Thirty-two upregulated and 121 downregulated differentially expressed proteins were identified in the hepatobiliary neuroendocrine neoplasm samples. Among the upregulated proteins is galectin-1, a multivalent carbohydrate binding protein known to play a role in lung and pancreatic neuroendocrine neoplasia development and progression in humans. Drugs targeting the galectin family have shown promise as anticancer therapeutics in cervical cancer, prostate cancer, lung and pancreatic neuroendocrine neoplasia in human medicine. Galectin-1 may represent a novel treatment target in hepatobiliary neuroendocrine neoplasia in both humans and dogs.
2023-03-11 | PXD028822 | Pride
Project description:Thymic epithelial tumors are a group of neoplasms with heterogeneous histological features and clinical behavior. The identification of markers useful to predict patient prognosis and molecular targets for therapies is limited by a very little understanding of the biology of these neoplasms. We evaluated the copy number (CN) aberrations of genes involved in normal thymus development in thymic epithelial tumors, following the intriguing idea that the ectopic deregulation of genes relevant for proliferation and differentiation of embryonic cells, can contribute to tumor growth. Frequent CN losses of FOXC1 were observed in more aggressive tumors and correlated with a reduced protein expression; tumors negative for FOXC1 expression were associated with a shorter time to progression. In addition, FOXC1 showed tumor suppressor activity in in-vitro models. Our data indicate that FOXC1 loss can identify a group of thymic epithelial tumors with poor prognosis, possibly because its tumor suppressor properties. Two color array CGH of a series of 59 thymic epithelial tumors plus evaluation of 2 thymic carcinoma cell lines and one thymoma B1 cell line.
2013-05-03 | E-GEOD-23540 | biostudies-arrayexpress
Project description:To study feasibility of gene expression profiling from FFPE tissues using NuGen amplified mRNA hybridized on Affymetrix GeneChip Human Gene 1.0 ST arrays, we designed a pilot study utilizing samples from prostate cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. Five serous carcinoma and six clear cell carcinoma samples with technical replicates
2014-07-01 | E-GEOD-54807 | biostudies-arrayexpress