Whole genome gene expression analysis of clear-cell renal cell carcinoma samples
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Maxwell 16, Promega, HiScan, Illumina
ORGANISM(S): Homo sapiens
SUBMITTER: Michal Seweryn
PROVIDER: E-MTAB-6118 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Tissue samples in biobanks preserved by formalin-fixation and paraffin-embedding (FFPE) and/or optimal cutting temperature (OCT)-embedded and subsequently freezing are highly valuable in experimental studies where the results can be related to clinical parameters. Today, mass spectrometry (MS)-based proteomics is the method of choice for unbiased and relative comparison of the abundances of thousands of proteins present in biological samples. MS analysis of FFPE- and OCT-preserved tissue has been limited, but it is now approachable using newly developed protocols. However, it has not been clarified how the results from different preservation methods agrees and differ. In this study, we use a unique sample set of urinary bladder cancer tissues of two different tumor stages (Ta/T1 – non-muscle invasive and T2/T3 muscle invasive); upon sampling the tumors were divided and preserved by the two methods. Thereafter a protocol for parallel processing of the samples were applied after which the samples were analyzed with label free quantitative MS analysis. Over 700 and 1200 proteins were quantified in FFPE and OCT samples, respectively. Principal component analysis showed that the largest differences between samples are based on the preservation method, but this analysis could also classify the tumors into different stages in each preservation. The overlap of quantifiable proteins between the preservation methods were 84% when all proteins and full data set were taken into consideration, but only 41% on average when proteins from a specific tumor were analyzed. Proteins involved in mitochondrial function were overrepresented among proteins present in OCT data but missing in the FFPE data, indicating that these proteins are not well preserved by FFPE. Moreover, univariate analysis showed that HMGCS2 protein is uniquely quantified in Ta/T1 tumors in both FFPE and OCT data, and that LGALS1, ANXA5 and plastin proteins are upregulated in T2/T3 tumors compared to Ta/T1 tumors in both FFPE and OCT data, confirming the consistency between the data sets and suggesting these proteins as biomarkers. Finally, LGALS1 data were verified by immunohistochemistry staining of an independent data set.
2021-09-09 | PXD020194 | Pride
Project description:The purpose of the experiment was to determine an immune profile consisting of immune genes and cell types in high grade serous ovarian cancer tissue from patients with various lengths of progression free survival. Formalin fixed paraffin embedded (FFPE) tissue was screened for 80% cellularity and 20% viability, and ImmunoPrism® analysis was performed by Cofactor Genomics to determine immune cell type percentages and expression of a panel of immune genes. A multidimensional immune model was generated using machine learning that was associated with longer progression free survival.
2021-11-02 | E-MTAB-9743 | 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:Primitive neuroectodermal tumours of the central nervous system (CNS PNETs) are highly aggressive, poorly differentiated embryonal tumours occurring predominantly in young children. Using DNA methylation and gene expression profiling we have demonstrated that a significant proportion of institutionally diagnosed CNS PNETs display molecular profiles indistinguishable from those of various other well defined CNS tumour entities, facilitating diagnosis and appropiate therapy for children with these tumours. From the remaining fraction of CNS PNETs, we have identified four distinct new CNS tumour entities extending to other neuroepithelial tumours, each associated with a recurrent genetic alteration and particular histopathological and clinical features. These molecular entities, designated â??CNS Neuroblastoma with FOXR2 activation (CNS NB FOXR2)â??, â??CNS Ewing sarcoma family tumour with CIC alteration (CNS EFT CIC)â??, â??CNS high grade neuroepithelial tumour with MN1 alteration (CNS HGNET MN1)â??, and â??CNS high grade neuroepithelial tumour with BCOR alteration (CNS HGNET BCOR)â??, will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by these poorly differentiated CNS tumours. 586 brain tumor samples were profiled using the Illumina HumanMethylation450 BeadChip (450k) array.
2016-02-25 | E-GEOD-73801 | biostudies-arrayexpress
Project description:Surgical resection of colorectal cancers (CRC) that have not invaded beyond the bowel wall (i.e. Stage I) can achieve 5-year patient survival rates exceeding 90%. In the majority of Stage I cases with T1 (submucosal) or T2 (not beyond the muscularis propria) depth of tumour invasion, surgery alone is curative. However, for approximately 10% of resected T1/2 CRC, even though histopathology inspection of the tumour deems it to be restricted to the bowel wall, malignant cells are identified in draining lymph nodes, signifying local metastasis. These patients are classified with Stage IIIA disease and are at greater risk than Stage I patients whose tumours show similar invasive depth, but lack lymph node involvement. To counter the risk of distant malignant dissemination, Stage IIIA patients require more extensive treatment with adjuvant chemotherapy, while Stage I patients do not. In this study we aim to get a better understanding of the underlying biological pathways linked to lymph node metastasis (LNM) using discovery based MS (DIA) and RNASeq as well as IHC and PRM to verify possible protein marker. All of this was done on archival tissue samples (FFPE).
2021-01-14 | PXD020808 | Pride
Project description:Cutaneous melanoma is an increasingly common form of skin cancer. The molecular mechanisms regulating melanoma progression are not completely understood. We speculated that specific miRNAs may be involved in melanoma development. We compared the miRNA expression profiles of benign nevi and metastatic melanomas. Unsupervised hierarchical clustering demonstrated a distinct miRNA expression pattern in metastatic melanomas compared to nevi. We identified miRNAs that were differentially expressed in melanoma. Notably, miR-193b was significantly down-regulated in the melanoma tissue examined. Using functional studies we demonstrated that over-expression of miR-193b significantly reduced melanoma cell proliferation, and arrested cell at G1 phase. Further gene expression analysis revealed that miR-193b regulated targets involved in cell cycle. Cyclin D1 was down-regulated by miR-193b at both the mRNA and protein level. This is the first study to show that the miR-193b may reduce cell proliferation by directly repressing cyclin D1. Overall, our study suggests that miRNAs are dysregulated in metastatic melanoma, and that miR-193b may play an important role in melanoma. 8 benign nevi and 8 metastatic melanoma tissue samples were profiled by Agilent MicroRNA Microarray (V1.5).
2010-05-16 | E-GEOD-18509 | biostudies-arrayexpress
Project description:Methylation profiling was performed of human germ cell cancers of testicular and ovarian origin. The main goal of the study was to investigate chromosomal copy numbers and to assess differential methylation patterns.
2019-02-11 | E-MTAB-5842 | biostudies-arrayexpress
Project description:DNA from 136 resected breast cancer tissues from patients exposed to ioinising radiation and non-exposed controls was analysed for genomic copy number alterations. The two groups were compared for the delination of genomic copy number changes associated with exposure status.
2018-04-02 | E-MTAB-6176 | biostudies-arrayexpress
Project description:Pancreatic cancer is the fourth leading cancer-related death in United States. The clinical relevance of genomic imbalances in pancreatic cancer is uncertain. We performed array-comparative genomic hybridization (aCGH) in 44 resected pancreatic cancer specimens from a Korean cohort. We observed recurrent copy number gains were observed in chromosome 1q, 11q, 18q11.1-11.2, and 20q13.13; and losses in chromosome 2p, 9p, 10q, 14q, 15q, 18q12.2-23, 19q, 20q11.1, 21p, and 22q. High copy number gains, with log2 ratio >2.0, were observed in 4 cytobands, encoding genes such as G protein-coupled receptor 48, c-myc and gamma-catenin. By comparing the aCGH results of long survivors and short survivors, determined according to the median survival, we observed that loss of cytoband 18q22.3, encoding 5 genes, was the only alteration with significantly different frequencies. The copy number of the CPGL (Carboxypeptidase of glutamate-like) gene in cytoband 18q22.3 was found to be significantly associated with overall survival in univariate analyses (p=0.019 by log-rank test). This was subsequently assessed in the Italian cohort: 41 out of the 61 specimens carried deletion of the CPGL gene. Patients with deletion of the CPGL gene also had shorter overall survival (p=0.003 by log-rank test). Multivariate analysis of the two cohorts combined showed that loss of 18q22.3 / deletion of the CPGL gene was an independent poor prognostic factor for overall survival after adjusting for other factors which were found to impact the outcome (hazard ratio 2.72, p=0.0007). overexpression of the CPGL or its alternating splicing isoform CPGL-B in a pancreatic cancer cell lines resulted in slower proliferation of cells, G1 cell cycle arrest, and reduced migration activity. In conclusion, through aCGH analysis, we identified loss of 18q22.3 / deletion of the CPGL gene as potentially being an independent poor prognostic factor in resected pancreatic cancer. We further identified the CPGL gene as a potential tumor suppressor for pancreatic cancer cell lines. Array-comparative genomic hybridization was performed in 44 resected pancreatic cancer specimen from a Korean cohort. Genomic alteration relating to prognosis of the Korean cohort was further validated in a Italian cohort containing 61 resected pancreatic cancer specimens.
2011-04-21 | E-GEOD-28732 | 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