Limits...
Determining PTEN functional status by network component deduced transcription factor activities.

Tran LM, Chang CJ, Plaisier S, Wu S, Dang J, Mischel PS, Liao JC, Graeber TG, Wu H - PLoS ONE (2012)

Bottom Line: Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate.Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis.Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America.

ABSTRACT
PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways in human cancers. With many small molecule inhibitors that target PI3K-AKT-mTOR pathway being exploited clinically, sensitive and reliable ways of stratifying patients according to their PTEN functional status and determining treatment outcomes are urgently needed. Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate. In this study, we used network component analysis to identify 20 transcription factors (TFs) whose activities deduced from their target gene expressions were immediately altered upon the re-expression of PTEN in a PTEN-inducible system. Interestingly, PTEN controls the activities (TFA) rather than the expression levels of majority of these TFs and these PTEN-controlled TFAs are substantially altered in prostate cancer mouse models. Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis. Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types. Together, our findings reveal that TFAs may be used as "signatures" for predicting PTEN functional status and elucidate the transcriptional architectures underlying human cancers caused by PTEN loss.

Show MeSH

Related in: MedlinePlus

PTEN re-expression downregulates activities of c-MYC and LEF1 in PTEN-inducible PC3 cells.(A) Immunoblot showing PTEN expression levels under Doxycycline induction. (B) Bar graphs showing fold changes of c-MYC and LEF1 mRNA expression by qPCR analysis. (C and D) Bar graphs showing the target gene expression of c-MYC and LEF1 by qPCR analysis, respectively. *p<0.05 and **p<0.01.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3275574&req=5

pone-0031053-g002: PTEN re-expression downregulates activities of c-MYC and LEF1 in PTEN-inducible PC3 cells.(A) Immunoblot showing PTEN expression levels under Doxycycline induction. (B) Bar graphs showing fold changes of c-MYC and LEF1 mRNA expression by qPCR analysis. (C and D) Bar graphs showing the target gene expression of c-MYC and LEF1 by qPCR analysis, respectively. *p<0.05 and **p<0.01.

Mentions: To validate the PTEN-controlled TFs identified in PTEN inducible MEF cells, we employed another PTEN-inducible system, the PTEN human prostate cancer cell line PC3 [6], [25]. By using human cell line, we are able to link PTEN-controlled TFs in mouse model to human cancers. Similar to our observation in the inducible-PtenΔloxp/Δloxp MEFs, PTEN protein expression is significantly induced after 1 and 2 days of doxycycline treatment in the inducible-PTEN PC3 cells (Figure 2A). Using qPCR analysis, we found that the expression levels of c-MYC and LEF1 after PTEN re-expression in PC3 cells also echoed those from the MEF-derived data: c-MYC gene expression is down-regulated (p<0.05) while LEF1 expression level remained constant (Figure 1C and 2B). We also measured the total protein level of c-MYC and phosphorylated to total protein ratios of STAT6 and c-JUN and found no substantial changes in c-MYC and STAT6 after PTEN re-expression (Figure S1B). In contrast, the ratio of phospho-c-JUN to total c-JUN is reduced by more than 2-fold after PTEN re-expression, consistent with our previous study [26].


Determining PTEN functional status by network component deduced transcription factor activities.

Tran LM, Chang CJ, Plaisier S, Wu S, Dang J, Mischel PS, Liao JC, Graeber TG, Wu H - PLoS ONE (2012)

PTEN re-expression downregulates activities of c-MYC and LEF1 in PTEN-inducible PC3 cells.(A) Immunoblot showing PTEN expression levels under Doxycycline induction. (B) Bar graphs showing fold changes of c-MYC and LEF1 mRNA expression by qPCR analysis. (C and D) Bar graphs showing the target gene expression of c-MYC and LEF1 by qPCR analysis, respectively. *p<0.05 and **p<0.01.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3275574&req=5

pone-0031053-g002: PTEN re-expression downregulates activities of c-MYC and LEF1 in PTEN-inducible PC3 cells.(A) Immunoblot showing PTEN expression levels under Doxycycline induction. (B) Bar graphs showing fold changes of c-MYC and LEF1 mRNA expression by qPCR analysis. (C and D) Bar graphs showing the target gene expression of c-MYC and LEF1 by qPCR analysis, respectively. *p<0.05 and **p<0.01.
Mentions: To validate the PTEN-controlled TFs identified in PTEN inducible MEF cells, we employed another PTEN-inducible system, the PTEN human prostate cancer cell line PC3 [6], [25]. By using human cell line, we are able to link PTEN-controlled TFs in mouse model to human cancers. Similar to our observation in the inducible-PtenΔloxp/Δloxp MEFs, PTEN protein expression is significantly induced after 1 and 2 days of doxycycline treatment in the inducible-PTEN PC3 cells (Figure 2A). Using qPCR analysis, we found that the expression levels of c-MYC and LEF1 after PTEN re-expression in PC3 cells also echoed those from the MEF-derived data: c-MYC gene expression is down-regulated (p<0.05) while LEF1 expression level remained constant (Figure 1C and 2B). We also measured the total protein level of c-MYC and phosphorylated to total protein ratios of STAT6 and c-JUN and found no substantial changes in c-MYC and STAT6 after PTEN re-expression (Figure S1B). In contrast, the ratio of phospho-c-JUN to total c-JUN is reduced by more than 2-fold after PTEN re-expression, consistent with our previous study [26].

Bottom Line: Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate.Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis.Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, California, United States of America.

ABSTRACT
PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways in human cancers. With many small molecule inhibitors that target PI3K-AKT-mTOR pathway being exploited clinically, sensitive and reliable ways of stratifying patients according to their PTEN functional status and determining treatment outcomes are urgently needed. Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate. In this study, we used network component analysis to identify 20 transcription factors (TFs) whose activities deduced from their target gene expressions were immediately altered upon the re-expression of PTEN in a PTEN-inducible system. Interestingly, PTEN controls the activities (TFA) rather than the expression levels of majority of these TFs and these PTEN-controlled TFAs are substantially altered in prostate cancer mouse models. Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis. Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types. Together, our findings reveal that TFAs may be used as "signatures" for predicting PTEN functional status and elucidate the transcriptional architectures underlying human cancers caused by PTEN loss.

Show MeSH
Related in: MedlinePlus