Unknown,Transcriptomics,Genomics,Proteomics

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The discovery and validation of ten-gene prognostic classifier in gastric cancer by whole genome expression profiling

ABSTRACT: The aim of this study is to identify and verify a prognosis set that is able to distinguish patient overall survival status based on whole genome expression profiling. Using Illumina HumanWG-6 beadarray, we analyzed the expression of 47,296 transcripts in two groups of gastric cancer patients who all underwent surgical resection. Thirty-nine of 46 samples in group one were used as a training set to discover candidates for overall survival prediction by using semi-supervised method, resulting in a panel of 10 genes as prognosis markers. This 10-marker set classified each case into a low or a high risk group with significantly different survival times (P = 0.000047) and maintained independent prognostic value in multivariate analysis. These 10 candidates were then verified in a fully independent validation set comprising 33 samples (P = 0.0009). Furthermore, the prognosis was consistent with the classical TNM staging system, and showed even better prediction. Interestingly, six of ten survival markers are ribosomal proteins, suggesting a possible association between deregulation of ribosome-related expression and poor prognosis. In conclusion, by whole genome expression profiling, 10 markers, including 6 ribosomal proteins, for overall survival prognosis of gastric cancer were found and validated, and which may be parallelly used with the TNM system. We investigated the transcriptome profiles of gastric cancer patients with different prognosis. Thirty-nine patients from first batch samples were used to discover prognostic markers and another 33 samples from batch two were used for validation.

ORGANISM(S): Homo sapiens

SUBMITTER: zheng zhang

PROVIDER: E-GEOD-21983 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling.

Zhang Yue-Zheng YZ Zhang Lian-Hai LH Gao Yang Y Li Chao-Hua CH Jia Shu-Qin SQ Liu Ni N Cheng Feng F Niu De-Yun DY Cho William Cs WC Ji Jia-Fu JF Zeng Chang-Qing CQ

World journal of gastroenterology 20110401 13

<h4>Aim</h4>To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis.<h4>Methods</h4>Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we analyzed the expression of 47,296 transcripts in two batches of gastric cancer patients who underwent surgical resection. Thirty-nine samples in the first batch were used as the training set to discover candidate markers correlated to overall survival, and thirty-three ...[more]

PMID: 21483631

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Project description:Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression. Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy. Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression. Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy. Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression. Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.

Dataset Information

The discovery and validation of ten-gene prognostic classifier in gastric cancer by whole genome expression profiling

Publications

Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling.

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