Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Global gene expression analysis of human colorectal cancer tissue

ABSTRACT: Generally, cancer tissue is palpated as a hard mass. On the other hand, it is not clear the nature of elasticity in cancer tissue. The aim in this study is to evaluate clinical utility of measuring elastic module in colorectal cancer tissue. Using a tactile sensor, we measured the elastic module of 106 surgically resected colorectal cancer tissues. The data of the elastic module were compared with the clinicopathological findings including stromal features represented by azan and α-SMA positive area ratio in tumor area. Finally cDNA microarray profile of the tumor with high elastic module was compared with that with low elastic module Higher elastic module in tumor was associated with pathological T-, N- and M-Stage (p < 0.001, p = 0.001 and p = 0.011, respectively). Patients with high elastic module showed shorter disease free survival than patients with low elastic module. The elastic module showed strongly positive correlation with azan positive area ratio (r = 0.908) and α-SMA positive area ratio (r = 0.921). Finally, the cDNA microarray data of the tumor with high elastic module revealed distinct gene expression profile from that with low elastic module. Assessment of elasticity of colorectal cancer tissue can be available for more accurate clinical stage or prognosis estimation. Distinct phenotypical feature of the high elastic module tumor and their strong association with stromal feature seemed to be suggesting the existence of biological mechanism involved in this phenomenon, which may contribute to the future therapy. We selected four samples from the highest and the lowest EM with RIN > 6.0 measured with a 2100 Bioanalyzer (Aligent Tochnologies, Santa Clara, CA, USA) and with stage II (pTNM pathologic classification). We excluded one sample in each group because of high GAPDH.

ORGANISM(S): Homo sapiens

SUBMITTER: Shingo Kawano

PROVIDER: E-GEOD-65222 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Wiskott-Aldrich syndrome (WAS) predisposes patients to leukemia and lymphoma. WAS is caused by mutations in the protein WASP which impair its interaction with the WIPF1 protein. Here, we aim to identify a module of WIPF1-coexpressed genes and to assess its use as a prognostic signature for colorectal cancer, glioma, and breast cancer patients. Two public colorectal cancer microarray data sets were used for discovery and validation of the WIPF1 co-expression module. Based on expression of the WIPF1 signature, we classified more than 400 additional tumors with microarray data from our own experiments or from publicly available data sets according to their WIPF1 signature expression. This allowed us to separate patient populations for colorectal cancers, breast cancers, and gliomas for which clinical characteristics like survival times and times to relapse were analyzed. Groups of colorectal cancer, breast cancer, and glioma patients with low expression of the WIPF1 co-expression module generally had a favorable prognosis. In addition, the majority of WIPF1 signature genes are individually correlated with disease outcome in different studies. Literature gene network analysis revealed that among WIPF1 co-expressed genes known direct transcriptional targets of c-myc, ESR1 and p53 are enriched. The mean expression profile of WIPF1 signature genes is correlated with the profile of a proliferation signature. The WIPF1 signature is the first microarray-based prognostic expression signature primarily developed for colorectal cancer that is instrumental in other tumor types: low expression of the WIPF1 module is associated with better prognosis. We used microarrays for the validation of a WIPF1 co-expression module which was developed on two publically available datasets. Keywords: disease state analysis For the generation of our own microarray data set, 62 CRC patients undergoing elective standard oncological resection at the Department of General, Vascular and Thoracic Surgery, Campus Benjamin Franklin, Charité, were prospectively recruited.

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Global gene expression analysis of human colorectal cancer tissue

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