Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Prostate cancer specific gene expression

ABSTRACT: To identify prostate cancer-specific gene expression, we have employed whole cDNA microarray expression profiling between benign prostate hypertrophy and prostate cancer. We performed needle biopsy of patients with prostatic hyperplasia who were suspected as prostate cancer for minor high level (4.0-10 ng/ml). As a result of needle biopsy, we used the tissue of patients with prostatic hyperplasia that prostate cancer was denied for cDNA microarry analysis. Furthermore, we also performed needle biopsy of patients that prostate cancer should have been strongly suspected because of high PSA. Needle biopsies were performed after we obtained informed consent from patients with the document approved from the Graduate School of Medical Science, Kanazawa University. Gene expression profile was determied in each of normal prostate samples and prostate cancer samples. Then the profiles were compared between normal prostate samples and prostate cancer samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Atsushi Mizokami

PROVIDER: E-GEOD-30994 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

SOD3 acts as a tumor suppressor in PC-3 prostate cancer cells via hydrogen peroxide accumulation.

Kim Jungim J Mizokami Atsushi A Shin Minkyoung M Izumi Kouji K Konaka Hiroyuki H Kadono Yoshifumi Y Kitagawa Yasuhide Y Keller Evan T ET Zhang Jian J Namiki Mikio M

Anticancer research 20140601 6

<h4>Background</h4>The functions of superoxide dismutase-3 (SOD3), which acts on the cell surface and protects cells from oxidative stress, remain uncertain in the progression of prostate cancer.<h4>Materials and methods</h4>To verify SOD3 expression in human prostate tissue, immunohistochemistry was performed using tissue microarrays. To investigate the effects of SOD3 on proliferation, migration, and invasion, SOD3 was overexpressed and recombinant SOD3 was employed in PC-3 prostate cancer cel ...[more]

PMID: 24922645

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Project description:Intra-tumor heterogeneity (ITH) has been studied at the morphologic, genomic, and transcriptomic level, but not proteomic level. Recent advances in mass spectrometric (MS) proteome quantification techniques, exemplified by SWATH-MS, a massively parallel targeting method, now also support precise quantitative proteomic comparisons across multiple samples, thus identifying molecular and implied functional differences. Here we used SWATH-MS to analyze the proteome profiles of a set of fresh-frozen prostate tissue samples derived from radical prostatectomy specimens. A high confidence set of 1,906 proteins were consistently quantified across 60 biopsy-level tissue samples from three prostatectomy patients, each consisting of 1.0 mm punch biopsies from histologically malignant (acinar and ductal adenocarcinoma) and matching benign prostatic hyperplasia tissues. The quantitative protein profiles allowed independent quantification of the degree of intra-tumor heterogeneity for each protein in benign and malignant tissues. We found that while majority of the proteins showed comparably low intra-tumor variability, 122 proteins were highly variable in malignant and/or matching benign tissues. We observed that proteins that varied between patients or tissue types also tended to be highly variable within prostate tissues, suggesting that these variability patterns will be a critical selection criterion in future protein biomarker studies. The data also permitted investigation of the heterogeneity of multiple biochemical pathways. The high variability of several of the pathways, including Glypican-1 network, alpha-linolenic acid metabolism and celecoxib pathway, explained contradictory results regarding them in the literature. In conclusion, we demonstrated a methodology for investigating proteomic intra-tumor heterogeneity from biopsy-level tissue samples, and quantified the degree of intra-tumor heterogeneity of 1,906 proteins in prostate tumors. The method and data presented here have advanced our understanding of tumor biology and offered critical insights for future biomarker development.

Dataset Information

Prostate cancer specific gene expression

Publications

SOD3 acts as a tumor suppressor in PC-3 prostate cancer cells via hydrogen peroxide accumulation.

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