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Providing tools that aid cancer detection

Using the Oncomine™ Platform to better understand cancer mechanisms and help inform prognosis

The Impact of PTEN Deletions
Oncogene-induced senescence (OIS) occurs when activated oncogenes suppress cell proliferation, rather than stimulating cell growth. OIS was first detected in cell-transfection experiments, and later in the prostate of young mice with an inactivated PTEN tumor suppressor gene. PTEN inhibits the PI3K pathway and is often deleted in cancer. Scientists found that loss of one PTEN allele increased proliferation, while loss of both alleles leads to prostatic intraepithelial neoplasia (PIN) and senescence [1]. In contrast, PTEN/TP53 double-null mutations result in an aggressive proliferation that was lethal in all mice tested. However, none of the double-mutant mice tested had distant metastases. 

SMAD4 and the Transition to Metastasis
A better understanding of the PIN-to-metastasis transition was uncovered in a second study in which authors subjected both wild type prostate and PTEN-null prostate RNA to gene expression microarray analysis, and found high levels of SMAD4 in the PTEN-null senescent samples [2]. SMAD4 is a DNA-binding protein that alters the transcription of downstream genes, suggesting that genes in the metastatic pathway may have SMAD-binding elements (SBEs). When SMAD4 was queried using Oncomine™ applications, it was found to be under-expressed in metastatic samples as compared to prostate carcinoma samples.

Identifying SMAD4 Targets
To test the hypothesis that high levels of SMAD4 maintain senescence and impede cancer progression, the authors created a PTEN/SMAD4 double-null mouse. As expected, these mice exhibited increased proliferation, reduced survival, and distant metastases. Further use of the Oncomine™ applications identified putative SMAD4 target genes, by looking for genes that correlate cancer progression with cell cycle regulation, and cancer progression with cell movement. The cell cycle regulator CCND1 and the cell movement gene SPP1 were identified and later confirmed to be physically-linked to the SMAD4 promoter using chromatin immunoprecipitation (Ch-IP) assays. 

Predicting Metastatic Potential
Putting all the pieces together, the authors show that the evaluation of PTEN, SMAD4, CCND1, and SPP1 predicts metastatic potential in 405 actual tumor samples, greatly outperforming the Gleason Score. This study is particularly notable in that it not only advances our understanding of key cancer mechanisms but also informs the development of better prognostic assays

1. Chen Z, Trotman LC, Shaffer D, et al. (2005) Crucial role of p53-dependent cellular senescence in suppression of Pten-deficient tumorigenesis. Nature 436:725–730.
2. Ding Z, Wu CJ, Chu GC, et al. (2011) SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression. Nature 470:269–273.

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Cancer Genomics Data Analysis
Oncomine™ Cancer Genomics Data Analysis Library