We have recently discovered a novel means of gene regulation whereby both protein-coding and non-coding RNAs are able to cross-talk through a new RNA language. In this new regulatory dimension, both protein-coding and non-coding RNAs (e.g. pseudogenes) can communicate with each other by competing for common microRNAs, hence acting as "competing endogenous RNAs" or ceRNAs. We have described several ceRNAs that regulate the tumor suppressor PTEN, thereby ascribing tumor suppressive functions to numerous cancer-unrelated mRNAs and non-coding RNAs. Moreover, we have developed a methodology to computationally predict ceRNAs for cancer-associated genes based upon the identity of their microRNA response elements (MREs), which are the foundation of this new language. This allows for the prediction and identification of novel putative tumor suppressors and oncogenes, and, critically, for the functionalization of the entire cancer-relevant transcriptome. We therefore propose to further characterize oncogenic and tumor suppressive ceRNA networks in vitro. Additionally, to explore the function of ceRNAs in basic biology in vivo, we have created a series of mouse models that express pseudogenes or 3'UTRs or lack established PTEN ceRNAs in an inducible manner. We will cross these mice to existing mouse models of cancer to characterize the contribution of ceRNAs to the malignant phenotype in vivo. We propose to address these outstanding questions pertaining to this new transformative biological dimension with the following specific aims: (1) to identify and functionally characteriz novel tumor suppressive PTEN ceRNAs as well as to analyze mouse models lacking bona fide PTEN ceRNAs such as ZEB2 and VHL;(2) to explore the effect of PTEN 3'UTR overexpression on the malignant phenotype elicited by either PTEN heterozygosity or overexpression of the PTEN targeting miR106b~25 cluster;(3) to analyze the ceRNA activity of the pseudogene BRAFps towards its ancestral gene, the proto-oncogene BRAF, in vitro and in vivo and its contribution to cancer development. We strongly believe that our application is both highly innovative and timely, with the potential to significantly further our understanding of this novel process of gene regulation in cancer genetics and biology.

Public Health Relevance

We have recently discovered a novel mode of gene regulation that is based on a new competitive endogenous RNA (ceRNA) language. Protein-coding and non-coding ceRNAs can cross talk by competing for microRNAs, which constitute the words of the ceRNA language. On the basis of this new theory, we use computational predictions and experimental validation to unravel extensive regulatory networks that impact the expression of prominent cancer genes, thus adding numerous novel players to the list of putative tumor suppressors and oncogenes. This application outlines an experimental strategy to further characterize, in vivo, the ceRNA biological dimension, with specific focus on the ceRNA networks of the critical tumor suppressor PTEN and the proto-oncogene BRAF.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA170158-03
Application #
8701257
Study Section
Special Emphasis Panel (ZCA1-SRLB-9 (M1))
Program Officer
Mietz, Judy
Project Start
2012-09-18
Project End
2016-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
3
Fiscal Year
2014
Total Cost
$350,219
Indirect Cost
$148,944
Name
Beth Israel Deaconess Medical Center
Department
Type
DUNS #
071723621
City
Boston
State
MA
Country
United States
Zip Code
02215
Karreth, Florian A; Ala, Ugo; Provero, Paolo et al. (2014) Pseudogenes as competitive endogenous RNAs: target prediction and validation. Methods Mol Biol 1167:199-212
Tay, Yvonne; Rinn, John; Pandolfi, Pier Paolo (2014) The multilayered complexity of ceRNA crosstalk and competition. Nature 505:344-52
Tay, Yvonne; Karreth, Florian A; Pandolfi, Pier Paolo (2014) Aberrant ceRNA activity drives lung cancer. Cell Res 24:259-60
Ala, Ugo; Karreth, Florian A; Bosia, Carla et al. (2013) Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci U S A 110:7154-9
Taulli, Riccardo; Loretelli, Cristian; Pandolfi, Pier Paolo (2013) From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition. Nat Struct Mol Biol 20:541-3
Karreth, Florian A; Pandolfi, Pier Paolo (2013) ceRNA cross-talk in cancer: when ce-bling rivalries go awry. Cancer Discov 3:1113-21