Gene expression profiles of 48 normal and 47 prostate tumor tissue samples
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ABSTRACT: Large-scale gene expression profiles were investigated in 48 normal and 47 prostate tumor tissue samples using Affymetrix GeneChip Exon 1.0 ST microarrays. Gene expression profiling of human prostate samples using Affymetrix Human Exon 1.0 ST arrays Two disease subtype analyses were performed: - Prostate Tumor vs Benign - TMPRSS2-ERG fusion-positive vs fusion-negative prostate tumors
Project description:The use of Nitric Oxide as a Radiosensitiser of Hypoxic Prostate Cancer Characterized by Data Independent Label-free Ion Mobility LC-MS
Project description:The occurrence of cancer is not equally distributed across the three zones of the prostate gland; the peripheral (PZ), central and transition zones (TZ). The majority (~70%) of diagnosed prostate cancer (PCa) is found in the PZ compared to the TZ. In this study we comprehensively measure whole genome expression by next-generation sequencing of the PZ and TZ from prostate tissue. Our aim was to identify the molecular and metabolic differences between the two zones that could underlie the differential susceptibility to PCa incidence. Following histological assessment of tissue adjacent to the biopsies used for RNAsequencing we identified 4 out of the 18 samples to be cancerous. Although these are included in the ArrayExpress submission, they were not included in the final analysis of data that reported the molecular differences between morphologically normal peripheral and transition zones.
Project description:The identification of novel oncogenic and druggable targets in patient subgroups with poor prognosis may help to develop corresponding targeted therapy approaches. Microarray data analyses of 59 prostate cancer and 39 benign tissue samples revealed major transcriptional differences. More than 5.000 genes were identified to be differentially expressed between matched tumor and benign samples. In the prostate cancer samples we identified 144 differentially expressed associated with Gleason pattern. Illumina microarray experiments were done from of 59 prostate cancer and 39 matched benign tissue samples. We analyzed for differentially expressed genes between tumor and benign tissues, and between tumors with higher Gleason patter (4+3 and higher) against lower Gleason patter (3+4 and lower).
Project description:Deregulated expression of miRNAs contributes to prostate cancer progression. This study is aimed to identify which miRNA(S) is (are) asociated with prostate cancer aggressiveness. Prostate cancer tissues and matched adjacent normal tissue were used to isolate total RNA. miRNA expressions were analyzed by miRNA Microarray assay.
Project description:We systematically dissected prostetectamy samples from three men with locally advanced prostate cancer, isolating histologically benign tissue and spatially separated tumour samples. In total 24 samples (including blood samples) were profiled using Infinium HumanMethylation450k arrays.
Project description:ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene. 48 Prostate cancer samples from radical prostatectomies were included in this study. These samples contained more than 70% cancer and less than 30% stromal tissue. Each sample was analyzed once.
Project description:MicroRNAs are small RNA molecules of about 21-25 nucleotides that regulate gene expression via posttranscriptional inhibition of protein synthesis. They play a vital role in the process of tumorigenesis. To identify and characterize the diagnostic potential of miRNAs in prostate cancer, a leading cause of tumor mortality, we performed microarray based screening of miRNA expression profiles. We selected 20 cases of moderately differentiated prostate cancer and generated pairs of tumor and corresponding normal tissue by microdissection
Project description:In order to examine the impact our probe filtering efforts might have on the analysis of real-world primary data, we analyzed clinical prostate cancer specimens. This included profiling of four prostate tumour tissue samples and four benign prostate tissues using the Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip. These samples were used to explore the effects on analysis with and without a probe filtering. Four tumour samples containing Gleason 6 cancer and four benign samples from other prostate glands containing Gleason 6 cancer were selected for study. Tissue samples were cryosectioned for histopathological assessment. Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 (HM450K bead array) BeadChip. Raw intensity data was generated using an iScan microarray reader (Illumina).