Similar Datasets
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:Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignany and currently the fourth leading cause of cancer related death worldwide. Circular RNAs (circRNAs) are a kind of novel noncoding RNA with a covalently circular structure arise from the non-canonical splicing of precursor-mRNA(pre-mRNA). To identify circRNAs involved in the progression of PDAC, next-generation sequencing (NGS) was performed in five paired PDAC and normal adjacent tissues. Our results suggest that the differential expressed circRNAs in PDAC tissues and normal adjacent tissues associated with the metastasis of PDAC.
2019-08-29 | GSE136569 | GEO
Project description:We report on the application of focused stromal cell single cell sequencing on paired adjacent and NSCLC tissue from 15 patients.
2022-08-12 | GSE183219 | GEO
Project description:Proteomics is a dynamic field emerged dramatically the post genomic era which has been extensively employed to study altered protein expression to gain insight into the development process and pathways involved in cancer and uncover potential protein markers. Membrane proteomes of an expanded cohort of paired CRC and adjacent non-tumorigenic tissues (1 female and 7 males) were profiled using high resolution nanoLC-MS/MS-based proteomics, which identified 1,000-1,300 proteins in each of the two tissue types. 184 proteins were differentially expressed (P < 0.05, fold change > 1.5); 69 proteins were up- regulated and 115 proteins were down-regulated in the CRC tissues relative to non-tumorigenic tissues.
2016-06-15 | PXD001676 | Pride
Project description:In this study, we performed laser capture microdissection (LCM) of PDAC samples to define their cancer- and stroma-specific molecular subtypes and identify a prognostic gene expression signature for short-term and long-term survival. LCM and RNA-seq analysis of cancer and adjacent stroma of 19 treatment-naïve PDAC tumors were performed. Gene expression signatures were tested for their robustness in a large independent validation set. An RNA in situ hybridization (RNA-ISH) assay with pooled probes for genes associated with disease-free survival (DFS) was developed to probe 111 PDAC tumor samples. Gene expression profiling identified four subtypes of cancer cells (C1-C4) and three subtypes of cancer-adjacent stroma (S1-S3). These stroma-specific subtypes were associated with DFS (p=5.55E-07), with S1 associated with better prognoses when paired with C1 and C2. Thirteen genes were found to be predominantly expressed in cancer cells and corresponded with DFS in a validation using existing RNA-seq datasets. A second validation on an independent cohort of patients using RNA-ISH probes to six of these prognostic genes demonstrated significant association with overall survival (median 17 versus 25 months; p<0.02). Our results identified specific signatures from the epithelial and the stroma components of PDAC, which add clarity to the nature of PDAC molecular subtypes and may help predict survival.
2021-06-30 | GSE164665 | GEO
Project description:Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina). 167 pancreatic tumors (PDAC) x 29 adjacent -non tumor samples.
2014-07-08 | E-GEOD-49149 | biostudies-arrayexpress
Project description:Inflammation has been identified as an important factor in cancer development and progression, including colorectal cancer [CRC]. To determine the role of inflammation and the specific contribution of activated fibroblasts in cancer development and progression we analyzed six human CRC tissue specimens and paired normal adjacent mucosa samples by LS/MS-MS. Amongst other, indeed several inflammation associated proteins were found differentially expressed compared to normal colonic mucosa. Two candidate molecules, SPARC and THBS2 were recently identified as proteins of a fibroblast inflammation signature. Analysis of public available RNA expression datasets revealed, that the mRNA of both SPARC and THBS2 are upregulated in CRC, typically in association with the CRC consensus molecular subtype 4 [CMS4]. Immunohistochemistry staining also demonstrated upregulation of SPARC and THBS2 in the tumor stroma compared to normal adjacent mucosa and indicated co-localization with the mesenchymal marker [alpha]SMA. In vitro 3D co-culture experiments with human colon derived fibroblasts and CRC cell lines resulted in enhanced SPARC and THBS2 protein levels when both cell types were cultivated in direct physical contact, compared to fibroblasts or cancer cells alone. This study demonstrates the feasibility of detecting tumor-specific signatures by LC-MS/MS and compatibility with RNA expression datasets. We identified an inflammation signature in CRC tissue and the data emphasized the contribution of activated fibroblasts in these events.
2018-10-17 | PXD006776 | Pride
Project description:We report a comprehensive proteomic analysis of diffuse-type gastric cancer (DGC) (n=83), intestinal-type gastric cancer (IGC) (n=102), mixed-type gastric cancer (MGC) (n=11), and paired normal adjacent tissues (NATs), including data obtained by proteomics, phospho-proteomics profiling and TFs activity profiling.
2022-11-18 | PXD038214 |
Project description:Although multi-omics studies of glioblastoma (GBM) have improved understanding of its biology nature and accelerated targeted therapy, data for paired adjacent normal tissues remains limited. Here, we report transcriptomes from 2 paired and 1 non-paired tumor and adjacent normal tissues (NAT) of glioblastoma (GBM) patients sequenced using Illumina Novaseq platform, and 150 bp paired-end reads were generated. This dataset provides a resource of paired GBM and normal tissues to identify novel tumor-specific oncogenes or tumor-suppressor genes.
2023-10-01 | GSE184643 | GEO
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