Pseudogene Journal Club Presentation
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Transcript of Pseudogene Journal Club Presentation
A Coding-Independent Function of Gene and Pseudogene mRNAs Regulates Tumour Biologyby Poliseno, Salmena, and Pandolfi
Krishna Doppalapudi, Lucas Man, Samantha Margulies, Patty Yau
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Introduction• PTEN is a tumor suppressor gene
▫ Its protein product is a phosphatase which regulates the cell cycle by preventing cells from dividing too rapidly
▫ Mutations in this gene are found in many cancers
• PTENP1 is the pseudogene of PTEN▫ Pseudogenes are relatives of known
genes that have lost their ability to be translated into protein
▫ Once considered nonfunctional• PTEN and PTENP1 mRNA transcripts
show homology ▫ Dark grey area is the highly conserved
region ▫ Colored lines show similar miRNA
binding sites
PTEN
PTENP1
Intro
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Introduction•microRNAs: class of small non-coding
RNAs•miRNAs bind to sequences in the 3’ UTR
of target mRNAs, resulting in gene silencing
Intro
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Competition for miRNA binding
•miRNAs can bind to either PTEN or PTENP1 pseudogene
miRNAs
PTEN
PTENP1
Intro
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Main Points of the Paper
1. PTENP1 is also targeted by PTEN-targeting miRNAs
2. The 3’ UTR of PTENP1 has tumor suppressive activity
3. PTENP1 levels influence downregulation of PTEN in cancer cells
4. PTEN/PTENP1 model should work for other genes
Main Pts
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
1. PTENP1 is targeted by PTEN-targeting miRNAs
A. PTEN is protected from miRNA binding by PTENP1
B. Homology▫ PTENP1 is one kb
shorter▫ Only 18 mismatches
throughout the entire coding sequence
C. Similar miRNA binding sites
▫ Perfectly conserved seed matches for miRNA 20, 21, 214, 19, 26
Results: Fig. 1
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
1. PTENP1 is targeted by PTEN-targeting miRNAs
D. In prostate cancer cells, miRNAs 19b and 20a suppressed PTEN and PTENP1 transcript abundance
▫ siLuc is used as a control▫ Blue and red bars show a
decrease in mRNA E. miRNA inhibitors (Imix)
increased PTENP1 and PTEN transcript abundance
▫ IC used as a control Without inhibitors
▫ Inhibitors cause derepression- miRNAs will not be able to silence the mRNA transcripts
Results: Fig. 1
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
A. PTENP1 3’ UTR expression derepressed PTEN transcription and translation
▫ Method: PTENP1 3’ UTR inserted into DU145 cells using retroviral vectors
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
B. Elevated PTEN expression is related to reduced phospho-AKT activity
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
B. Elevated PTEN expression is related to reduced phospho-AKT activity
C. Effect of derepressed PTEN is growth inhibition
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
B. Elevated PTEN expression is related to reduced phospho-AKT activity
C. Effect of derepressed PTEN is growth inhibition
D. PTENP1 3’ UTR is a more potent growth suppressor than PTEN
▫ Could function as a decoy for miRNAs that bind to other targets with tumour suppressive activities
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
E. Disruption of DICER blunts derepression of PTEN by PTENP1 3’ UTR
▫ Suggests PTENP1 3’ UTR requires mature miRNA for function
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
E. Disruption of DICER blunts derepression of PTEN by PTENP1 3’ UTR
▫ Suggests PTENP1 3’ UTR requires mature miRNA for function
F. Silencing both PTEN and PTENP1 showed strongest increase in cell proliferation
▫ Suggests additive roles for PTEN and PTENP1 in growth suppression
siRNA function in RNA interference to degrade mRNA, introducing siRNA can have the effect of “knocking-down” or “silencing” genes
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
E. Disruption of DICER blunts derepression of PTEN by PTENP1 3’ UTR
▫ Suggests PTENP1 3’ UTR requires mature miRNA for function
F. Silencing both PTEN and PTENP1 showed strongest increase in cell proliferation
▫ Suggests additive roles for PTEN and PTENP1 in growth suppression
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
G. siRNA knockdown decreased PTEN and PTENP1 mRNA
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
2. The 3’ UTR of PTENP1 has tumor suppressive activity
G. siRNA knockdown decreased PTEN and PTENP1 mRNA
H. siRNA knockdown also decreased PTEN protein abundance
Results: Fig. 2
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
3. PTENP1 levels influence downregulation of PTEN in cancer cells
A., B. PTEN and PTENP1 expression are co-regulated
Method: Quantitative RT PCR, measured by green fluorescence (Taqman)
Direct correlation between PTEN and PTENP1 expression in both normal tissue and tumour samples (r = 0.8087 and 0.7538; P<0.0001)
C. In colon cancer samples, independent copy number losses occur specifically in PTENP1 gene
Copy number losses in PTENP1 occur due to selective pressure in cancer
Results: Fig. 3
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
3. PTENP1 levels influence downregulation of PTEN in cancer cells
D. PTEN expression is downregulated in cancer cells
E. PTENP1 transcript levels regulate PTEN expression
▫ Direct correlation between log ratio of PTENP1 copy number vs. log10 PTEN expression intensity
1. r = 0.6105, P = 0.00922. r = 0.6056, P = 0.0129
Results: Fig. 3
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
4. Model should work for other genes
A. PTEN 3’ UTR derepresses PTENP1 mRNA and shows growth suppression
B. KRAS and its pseudogene show similar regulatory mechanisms.
▫ It is known that K1P 3’ UTR overexpression leads to increased levels of KRAS, and consequently cell proliferation and accelerated cell growth
Results: Fig. 4
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
4. Model should work for other genes
C. RNAs X and Y in this figure can be thought of as a pseudogene and its cognate protein coding gene.▫ In Case 1, the
downregulation of RNA X leads to increased binding sites for the miRNA on RNA Y, causing RNA Y to be repressed.
▫ In Case 2, both RNA X and RNA Y are in equilibrium
▫ In Case 3, RNA X is overexpressed and act as an miRNA sponge, this derepresses RNA Y
Results: Fig. 4
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Conclusion
•Scientists have discovered a new dimension by which cellular and tumor biology can be regulated
•Pseudogenes were once considered non-functional, but are now known to affect mRNA transcript abundance through a miRNA binding mechanism
Conclusion
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
References
•http://www.jyi.org/features/ft.php?id=392•http://
www.answersingenesis.org/tj/v17/i2/pseudogene.asp
•Nature, Vol 465, 24 June 2010, A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
Intro Main Pts Results: Fig. 1 Fig. 2 Fig. 3 Fig. 4 Conclusion
Questions